101
|
Zavadlav J, Marrink SJ, Praprotnik M. Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm. J Chem Theory Comput 2018; 14:1754-1761. [PMID: 29439560 DOI: 10.1021/acs.jctc.7b01129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to modified AT water models, such as the bundled-simple point charge (SPC) models, that use semiharmonic springs to restrict the relative movement of water molecules within a cluster. Those models can have a significant impact on the simulated biomolecules and can lead, for example, to a partial unfolding of a protein. In this work, we employ the recently developed alternative approach with a dynamical clustering algorithm, SWINGER, which enables a direct coupling of original unmodified AT and SCG water models. We perform an adaptive resolution molecular dynamics simulation of a Trp-Cage miniprotein in multiscale water, where the standard SPC water model is interfaced with the widely used MARTINI SCG model, and demonstrate that, compared to the corresponding full-blown AT simulations, the structural and dynamic properties of the solvated protein and surrounding solvent are well reproduced by our approach.
Collapse
Affiliation(s)
- Julija Zavadlav
- Computational Science & Engineering Laboratory , ETH Zurich , Clausiusstrasse 33 , CH-8092 Zurich , Switzerland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Matej Praprotnik
- Laboratory for Molecular Modeling , National Institute of Chemistry , Hajdrihova 19 , SI-1001 Ljubljana , Slovenia.,Department of Physics, Faculty of Mathematics and Physics , University of Ljubljana , Jadranska 19 , SI-1000 Ljubljana , Slovenia
| |
Collapse
|
102
|
Qiao B, Skanthakumar S, Soderholm L. Comparative CHARMM and AMOEBA Simulations of Lanthanide Hydration Energetics and Experimental Aqueous-Solution Structures. J Chem Theory Comput 2018; 14:1781-1790. [DOI: 10.1021/acs.jctc.7b01018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Baofu Qiao
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - S. Skanthakumar
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - L. Soderholm
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| |
Collapse
|
103
|
La Penna G, Chelli R. Structural Insights into the Osteopontin-Aptamer Complex by Molecular Dynamics Simulations. Front Chem 2018; 6:2. [PMID: 29441346 PMCID: PMC5797602 DOI: 10.3389/fchem.2018.00002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/08/2018] [Indexed: 12/17/2022] Open
Abstract
Osteopontin is an intrinsically disordered protein involved in tissue remodeling. As a biomarker for pathological hypertrophy and fibrosis, the protein is targeted by an RNA aptamer. In this work, we model the interactions between osteopontin and its aptamer, including mono- (Na+) and divalent (Mg2+) cations. The molecular dynamics simulations suggest that the presence of divalent cations forces the N-terminus of osteopontin to bind the shell of divalent cations adsorbed over the surface of its RNA aptamer, the latter exposing a high negative charge density. The osteopontin plasticity as a function of the local concentration of Mg is discussed in the frame of the proposed strategies for osteopontin targeting as biomarker and in theranostic.
Collapse
Affiliation(s)
- Giovanni La Penna
- Istituto di Chimica dei Composti Organometallici, Consiglio Nazionale delle Ricerche (CNR), Florence, Italy
| | - Riccardo Chelli
- Dipartimento di Chimica, Università di Firenze, Florence, Italy
| |
Collapse
|
104
|
Bagheri B, Baumeier B, Karttunen M. Getting excited: challenges in quantum-classical studies of excitons in polymeric systems. Phys Chem Chem Phys 2018; 18:30297-30304. [PMID: 27453482 DOI: 10.1039/c6cp02944b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) was performed to describe the conformational properties of diphenylethyne (DPE), methylated-DPE and poly para phenylene ethynylene (PPE). DFT calculations were employed to improve and develop force field parameters for MM/MD simulations. Many-body Green's function theory within the GW approximation and the Bethe-Salpeter (GW-BSE) equation were utilized to describe the excited states of the systems. The reliability of the excitation energies based on the MM/MD conformations was examined and compared to the excitation energies from DFT conformations. The results show an overall agreement between the optical excitations based on MM/MD conformations and DFT conformations. This allows for the calculation of excitation energies based on MM/MD conformations.
Collapse
Affiliation(s)
- Behnaz Bagheri
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Björn Baumeier
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.
| |
Collapse
|
105
|
Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 476] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
Collapse
Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| |
Collapse
|
106
|
Glova AD, Falkovich SG, Dmitrienko DI, Lyulin AV, Larin SV, Nazarychev VM, Karttunen M, Lyulin SV. Scale-Dependent Miscibility of Polylactide and Polyhydroxybutyrate: Molecular Dynamics Simulations. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01640] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Artyom D. Glova
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 St. Petersburg, Russia
| | - Stanislav G. Falkovich
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 St. Petersburg, Russia
| | - Daniil I. Dmitrienko
- Faculty
of Physics, Saint-Petersburg University, Ulyanovskaya str. 1, Petrodvorets, 198504 St. Petersburg, Russia
| | - Alexey V. Lyulin
- Theory
of Polymers and Soft Matter Group, Technische Universiteit Eindhoven, PO Box 513, 5600 MB Eindhoven, The Netherlands
| | - Sergey V. Larin
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 St. Petersburg, Russia
| | - Victor M. Nazarychev
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 St. Petersburg, Russia
| | - Mikko Karttunen
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 St. Petersburg, Russia
- Department
of Chemistry and Department of Applied Mathematics, Western University, 1151 Richmond St., London, Ontario, Canada N6A 5B7
| | - Sergey V. Lyulin
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoj
pr. V.O., 31, 199004 St. Petersburg, Russia
- Faculty
of Physics, Saint-Petersburg University, Ulyanovskaya str. 1, Petrodvorets, 198504 St. Petersburg, Russia
| |
Collapse
|
107
|
Doerr TP, Obolensky OI, Yu YK. Extending electrostatics of dielectric spheres to arbitrary charge distributions with applications to biosystems. Phys Rev E 2017; 96:062414. [PMID: 29347333 PMCID: PMC6312187 DOI: 10.1103/physreve.96.062414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Indexed: 11/07/2022]
Abstract
A previously developed classical model of electrostatic interactions, based on a formalism of dielectric spheres, which has been found to have surprising accuracy for S state atoms, is extended by allowing higher-order moments of the intrinsic charge distribution. Two methods to introduce the charge distribution (point moments at the center vs surface charge) are shown to be equivalent and are compared with another common model for polarizable atoms that utilizes polarizable point dipoles. Unlike the polarizable point dipole model, the polarizable spheres models do not suffer from a divergence at small separation of atoms and are easily generalized to higher multipoles.
Collapse
Affiliation(s)
- T. P. Doerr
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | | | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| |
Collapse
|
108
|
Manzoni F, Uranga J, Genheden S, Ryde U. Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations? J Chem Inf Model 2017; 57:2865-2873. [PMID: 29076739 DOI: 10.1021/acs.jcim.7b00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have investigated whether alchemical free-energy perturbation calculations of relative binding energies can be sped up by simulating a truncated protein. Previous studies with spherical nonperiodic systems showed that the number of simulated atoms could be reduced by a factor of 26 without affecting the calculated binding free energies by more than 0.5 kJ/mol on average ( Genheden, S.; Ryde, U. J. Chem. Theory Comput. 2012 , 8 , 1449 ), leading to a 63-fold decrease in the time consumption. However, such simulations are rather slow, owing to the need of a large cutoff radius for the nonbonded interactions. Periodic simulations with the electrostatics treated by Ewald summation are much faster. Therefore, we have investigated if a similar speed-up can be obtained also for periodic simulations. Unfortunately, our results show that it is harder to truncate periodic systems and that the truncation errors are larger for these systems. In particular, residues need to be removed from the calculations, which means that atoms have to be restrained to avoid that they move in an unrealistic manner. The results strongly depend on the strength on this restraint. For the binding of seven ligands to dihydrofolate reductase and ten inhibitors of blood-clotting factor Xa, the best results are obtained with a small restraining force constant. However, the truncation errors were still significant (e.g., 1.5-2.9 kJ/mol at a truncation radius of 10 Å). Moreover, the gain in computer time was only modest. On the other hand, if the snapshots are truncated after the MD simulations, the truncation errors are small (below 0.9 kJ/mol even for a truncation radius of 10 Å). This indicates that postprocessing with a more accurate energy function (e.g., with quantum chemistry) on truncated snapshots may be a viable approach.
Collapse
Affiliation(s)
- Francesco Manzoni
- Department of Theoretical Chemistry, Lund University, Chemical Centre , P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jon Uranga
- Department of Theoretical Chemistry, Lund University, Chemical Centre , P.O. Box 124, SE-221 00 Lund, Sweden
| | - Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre , P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre , P.O. Box 124, SE-221 00 Lund, Sweden
| |
Collapse
|
109
|
Takahashi KZ. Combined use of periodic reaction field and coarse-grained molecular dynamics simulations. I. phospholipid monolayer systems. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2016.1271948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kazuaki Z. Takahashi
- Multi-scale Soft-matter Simulation Team, Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| |
Collapse
|
110
|
Nishimura Y, Nakai H. Parallel implementation of efficient charge-charge interaction evaluation scheme in periodic divide-and-conquer density-functional tight-binding calculations. J Comput Chem 2017; 39:105-116. [DOI: 10.1002/jcc.25086] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Yoshifumi Nishimura
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
| | - Hiromi Nakai
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering; Waseda University, 3-4-1 Okubo, Shinjuku-ku; Tokyo 169-8555 Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho; Kawaguchi 332-0012 Japan
- ESICB, Kyoto University, Kyotodaigaku-Katsura; Kyoto 615-8520 Japan
| |
Collapse
|
111
|
Bojarowski SA, Kumar P, Dominiak PM. Interplay of point multipole moments and charge penetration for intermolecular electrostatic interaction energies from the University at Buffalo pseudoatom databank model of electron density. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:598-609. [PMID: 28762970 DOI: 10.1107/s2052520617005510] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
The strength of the University at Buffalo DataBank (UBDB) in Ees estimation is mainly due to charge overlap effects because the UBDB offers continuous representation of charge density which allows for a direct account of charge penetration in the derivation of electrostatic energies. In the UBDB model, these effects begin to play an important role at distances below twice the equilibrium distance and significantly increase as distances decrease. At equilibrium distances they are responsible for 30-50% of Ees for polar molecules and around 90% of Ees for nonpolar molecules. When the energy estimation from the UBDB is reduced to point multipoles, the results are comparable to point charges fitted to electrostatic potentials. On the other hand, particular components of energy from point multipole moments from the UBDB model are sensitive to the type of interaction and might be helpful in the characterization of interactions.
Collapse
Affiliation(s)
- Sławomir A Bojarowski
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Prashant Kumar
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Center, Department of Chemistry, University of Warsaw, ul. Zwirki i Wigury 101, 02-089 Warszawa, Poland
| |
Collapse
|
112
|
Ojeda-May P, Nam K. Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations. J Chem Theory Comput 2017. [PMID: 28628742 DOI: 10.1021/acs.jctc.7b00322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in CHARMM are described. The serial version of the code was first profiled to identify routines that required parallelization. Afterward, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM message passage interface (MPI) machinery. In the second approach, two different self-consistent field (SCF) energy convergence accelerators were implemented using density and Fock matrices as targets for their extrapolations in the SCF procedure. In the third approach, the entire QM/MM and MM energy routines were accelerated by implementing the hybrid MPI/open multiprocessing (OpenMP) model in which both the task- and loop-level parallelization strategies were adopted to balance loads between different OpenMP threads. The present implementation was tested on two solvated enzyme systems (including <100 QM atoms) and an SN2 symmetric reaction in water. The MPI version exceeded existing SE QM methods in CHARMM, which include the SCC-DFTB and SQUANTUM methods, by at least 4-fold. The use of SCF convergence accelerators further accelerated the code by ∼12-35% depending on the size of the QM region and the number of CPU cores used. Although the MPI version displayed good scalability, the performance was diminished for large numbers of MPI processes due to the overhead associated with MPI communications between nodes. This issue was partially overcome by the hybrid MPI/OpenMP approach which displayed a better scalability for a larger number of CPU cores (up to 64 CPUs in the tested systems).
Collapse
Affiliation(s)
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington , Arlington, Texas 76019-0065, United States
| |
Collapse
|
113
|
Liu C, Qi R, Wang Q, Piquemal JP, Ren P. Capturing Many-Body Interactions with Classical Dipole Induction Models. J Chem Theory Comput 2017; 13:2751-2761. [PMID: 28482664 PMCID: PMC5472369 DOI: 10.1021/acs.jctc.7b00225] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 11/29/2022]
Abstract
The nonadditive many-body interactions are significant for structural and thermodynamic properties of condensed phase systems. In this work we examined the many-body interaction energy of a large number of common organic/biochemical molecular clusters, which consist of 18 chemical species and cover nine common organic elements, using the Møller-Plesset perturbation theory to the second order (MP2) [ Møller et al. Phys. Rev. 1934 , 46 , 618 . ]. We evaluated the capability of Thole-based dipole induction models to capture the many-body interaction energy. Three models were compared: the original model and parameters used by the AMOEBA force field, a variation of this original model where the damping parameters have been reoptimized to MP2 data, and a third model where the damping function form applied to the permanent electric field is modified. Overall, we find the simple classical atomic dipole models are able to capture the 3- and 4-body interaction energy across a wide variety of organic molecules in various intermolecular configurations. With modified Thole models, it is possible to further improve the agreement with MP2 results. These models were also tested on systems containing metal/halogen ions to examine the accuracy and transferability. This work suggests that the form of damping function applied to the permanent electrostatic field strongly affects the distance dependence of polarization energy at short intermolecular separations.
Collapse
Affiliation(s)
- Chengwen Liu
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Rui Qi
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Qiantao Wang
- Key
Laboratory of Drug Targeting and Drug Delivery System of Education
Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - J.-P. Piquemal
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
- Laboratoire
de Chimie Théorique, Sorbonne Universités,
UPMC, UMR 7616 CNRS, Paris 75252, France
- Institut Universitaire
de France, Paris Cedex 05, 75231, France
| | - Pengyu Ren
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
114
|
HÖft TA, Alpert BK. FAST UPDATING MULTIPOLE COULOMBIC POTENTIAL CALCULATION. SIAM JOURNAL ON SCIENTIFIC COMPUTING : A PUBLICATION OF THE SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS 2017; 39:https://doi.org/10.1137/16M1096189. [PMID: 33088167 PMCID: PMC7574401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We present a numerical method to efficiently and accurately re-compute the Coulomb potential of a large ensemble of charged particles after a subset of the particles undergoes a change of position. Errors are bounded even after a large number of such shifts, making it practical for use in Monte Carlo Markov chain methods in molecular dynamics, computational astrophysics, computational chemistry, and other applications. The method uses truncated multipole expansions of the potential energy functional and a tree decomposition of the computational domain to reduce the computational complexity. Computational costs scale logarithmically in the size of the problem. Scaling, accuracy, and efficiency are confirmed with numerical experiments. The new method outperforms a direct calculation for moderate problem sizes.
Collapse
Affiliation(s)
- Thomas A HÖft
- Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105
| | - Bradley K Alpert
- National Institute of Standards and Technology, Boulder, Colorado 80305
| |
Collapse
|
115
|
Gao X, Fang J, Wang H. Kaiser-Bessel basis for particle-mesh interpolation. Phys Rev E 2017; 95:063303. [PMID: 28709276 DOI: 10.1103/physreve.95.063303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 06/07/2023]
Abstract
In this work, we introduce the Kaiser-Bessel interpolation basis for the particle-mesh interpolation in the fast Ewald method. A reliable a priori error estimate is developed to measure the accuracy of the force computation in correlated charge systems, and is shown to be effective in optimizing the shape parameter of the Kaiser-Bessel basis in terms of accuracy. By comparing the optimized Kaiser-Bessel basis with the traditional B-spline basis, we demonstrate that the former is more accurate than the latter in part of the working parameter space, say, a relatively small real-space cutoff, a relatively small reciprocal space mesh, and a relatively large truncation of basis. In some cases, the Kaiser-Bessel basis is found to be more than one order of magnitude more accurate.
Collapse
Affiliation(s)
- Xingyu Gao
- Laboratory of Computational Physics, Huayuan Road 6, Beijing 100088, People's Republic of China; Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094, People's Republic of China; and CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, Beijing 100088, People's Republic of China
| | - Jun Fang
- Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094, People's Republic of China and CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, Beijing 100088, People's Republic of China
| | - Han Wang
- Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094, People's Republic of China and CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, Beijing 100088, People's Republic of China
| |
Collapse
|
116
|
Kan Z, Zhu Q, Yang L, Huang Z, Jin B, Ma J. Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method. J Phys Chem B 2017; 121:4319-4332. [DOI: 10.1021/acs.jpcb.6b12647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zigui Kan
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of MOE, Nanjing University, Nanjing 210093, People’s Republic of China
- School
of Sciences, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Qiang Zhu
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of MOE, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Lijiang Yang
- Institute
of Theoretical and Computational Chemistry, College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Zhixiong Huang
- Research
Institute of Superconductor Electronics (RISE), School of Electronic
Science and Engineering, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Biaobing Jin
- Research
Institute of Superconductor Electronics (RISE), School of Electronic
Science and Engineering, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Jing Ma
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of MOE, Nanjing University, Nanjing 210093, People’s Republic of China
| |
Collapse
|
117
|
Verma P, Wang B, Fernandez LE, Truhlar DG. Physical Molecular Mechanics Method for Damped Dispersion. J Phys Chem A 2017; 121:2855-2862. [PMID: 28328203 DOI: 10.1021/acs.jpca.7b02384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Damped dispersion can be a significant component of the interaction energy in many physical and chemical processes, for example, physisorption and noncovalent complexation. For physically interpreting and modeling such processes, it is convenient to have an analytic method to calculate damped dispersion that is readily applicable across the entire periodic table. Of the available methods to calculate damped dispersion energy for interacting systems with overlapping charge distributions, we select symmetry-adapted perturbation theory (SAPT) as providing a reasonable definition, and of the possible analytic forms, we choose the D3(BJ) method. However, the available parametrizations of D3(BJ) include not only damped dispersion energy but also corrections for errors in specific exchange-correlation functionals. Here we present a parametrization that provides a physical measure of damped dispersion without such density functional corrections. The method generalizes an earlier method of Pernal and co-workers to all elements from hydrogen to plutonium.
Collapse
Affiliation(s)
- Pragya Verma
- Department of Chemistry, Nanoporous Materials Genome Center, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
| | - Bo Wang
- Department of Chemistry, Nanoporous Materials Genome Center, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
| | - Laura E Fernandez
- Department of Chemistry, Nanoporous Materials Genome Center, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Nanoporous Materials Genome Center, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota , 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431, United States
| |
Collapse
|
118
|
Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
Collapse
Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
119
|
Huang J, Mei Y, König G, Simmonett AC, Pickard FC, Wu Q, Wang LP, MacKerell AD, Brooks BR, Shao Y. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. J Chem Theory Comput 2017; 13:679-695. [PMID: 28081366 DOI: 10.1021/acs.jctc.6b01125] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.
Collapse
Affiliation(s)
- Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States.,Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Gerhard König
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, NRW Germany, EU
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Frank C Pickard
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California , 1 Shields Avenue, Davis, California 95616, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States.,Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| |
Collapse
|
120
|
Koziol L, Fried LE, Goldman N. Using Force Matching To Determine Reactive Force Fields for Water under Extreme Thermodynamic Conditions. J Chem Theory Comput 2016; 13:135-146. [DOI: 10.1021/acs.jctc.6b00707] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Koziol
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Nir Goldman
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| |
Collapse
|
121
|
Obolensky OI, Doerr TP, Ogurtsov AY, Yu YK. Can dielectric spheres accurately model atomic-scale interactions? EUROPHYSICS LETTERS 2016; 116:24003. [PMID: 31631925 PMCID: PMC6800739 DOI: 10.1209/0295-5075/116/24003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We calculate the polarization portion of electrostatic interactions at the atomic scale using quantum mechanical methods such as density functional theories (DFT) and the coupled cluster approach, and using classical methods such as a surface charge method and a polarizable force field. The agreement among various methods is investigated. Using the coupled clusters method CCSD(T) with large basis sets as the reference, we find that for systems comprising two to six atoms and ions in S-states the classical surface charge method performs much better than commonly used DFT methods with moderate basis sets such as B3LYP/6-31G(d,p). The remarkable performance of the classical approach comes as a surprise. The present results indicate that the use of a rigorous formalism of classical electrostatics can be better justified for determining molecular interactions at intermediate distances than some of the widely used methods of quantum chemistry. PACS numbers: 41.20.Cv,32.10.Dk, 87.10.Tf.
Collapse
Affiliation(s)
| | - T. P. Doerr
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - A. Y. Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| |
Collapse
|
122
|
Affiliation(s)
- John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| |
Collapse
|
123
|
Terrón-Mejía KA, López-Rendón R, Goicochea AG. Electrostatics in dissipative particle dynamics using Ewald sums with point charges. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:425101. [PMID: 27541198 DOI: 10.1088/0953-8984/28/42/425101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald-based methods, which have become some of the cornerstones upon which many other methods for the numerical computation of electrostatic interactions are based. However, their use with charge distributions rather than point charges requires the inclusion of ansatz for the solutions of the Poisson equation, since there is no exact solution known for smeared out charges. The interest in incorporating electrostatic interactions at the scales of length and time that are relevant for the study the physics of soft condensed matter has increased considerably. Using mesoscale simulation techniques, such as dissipative particle dynamics (DPD), allows us to reach longer time scales in numerical simulations, without abandoning the particulate description of the problem. The main problem with incorporating electrostatics into DPD simulations is that DPD particles are soft and those particles with opposite charge can form artificial clusters of ions. Here we show that one can incorporate the electrostatic interactions through Ewald sums with point charges in DPD if larger values of coarse-graining degree are used, where DPD is truly mesoscopic. Using point charges with larger excluded volume interactions, the artificial formation of ionic pairs with point charges can be avoided and one obtains correct predictions. We establish ranges of parameters useful for detecting boundaries where artificial formation of ionic pairs occurs. Lastly, using point charges we predict the scaling properties of polyelectrolytes in solvents of varying quality, and obtain predictions that are in agreement with calculations that use other methods and with recent experimental results.
Collapse
Affiliation(s)
- Ketzasmin A Terrón-Mejía
- Laboratorio de Bioingeniería Molecular a Multiescala, Facultad de Ciencias, Universidad Autónoma del Estado de México, Av. Instituto Literario 100, Toluca 50000, Estado de México, Mexico
| | | | | |
Collapse
|
124
|
Bereau T, Bennett WFD, Pfaendtner J, Deserno M, Karttunen M. Folding and insertion thermodynamics of the transmembrane WALP peptide. J Chem Phys 2016; 143:243127. [PMID: 26723612 DOI: 10.1063/1.4935487] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum-in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.
Collapse
Affiliation(s)
- Tristan Bereau
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - W F Drew Bennett
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum, 5600 MB Eindhoven, The Netherlands
| |
Collapse
|
125
|
Fingerhut BP, Costard R, Elsaesser T. Predominance of short range Coulomb forces in phosphate-water interactions—a theoretical analysis. J Chem Phys 2016. [DOI: 10.1063/1.4962755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| |
Collapse
|
126
|
Cisneros G, Wikfeldt KT, Ojamäe L, Lu J, Xu Y, Torabifard H, Bartók AP, Csányi G, Molinero V, Paesani F. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chem Rev 2016; 116:7501-28. [PMID: 27186804 PMCID: PMC5450669 DOI: 10.1021/acs.chemrev.5b00644] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 12/17/2022]
Abstract
Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.
Collapse
Affiliation(s)
| | - Kjartan Thor Wikfeldt
- Science
Institute, University of Iceland, VR-III, 107, Reykjavik, Iceland
- Department
of Physics, Albanova, Stockholm University, S-106 91 Stockholm, Sweden
| | - Lars Ojamäe
- Department
of Chemistry, Linköping University, SE-581 83 Linköping, Sweden
| | - Jibao Lu
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Yao Xu
- Lehrstuhl
Physikalische Chemie II, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Hedieh Torabifard
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Albert P. Bartók
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Gábor Csányi
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Valeria Molinero
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Francesco Paesani
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| |
Collapse
|
127
|
Simonson T, Roux B. Concepts and protocols for electrostatic free energies. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2015.1121544] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
128
|
Kratz EG, Duke RE, Cisneros GA. Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations. Theor Chem Acc 2016; 135:166. [PMID: 28367078 PMCID: PMC5373107 DOI: 10.1007/s00214-016-1923-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Taking long-range electrostatic effects into account in classical and hybrid quantum mechanics-molecular mechanics (QM/MM) simulations is necessary for an accurate description of the system under study. We have recently developed a method, termed long-range electrostatic corrections (LREC), for monopolar QM/MM calculations. Here, we present an extension of LREC for multipolar/polarizable QM/MM simulations within the LICHEM software package. Reaction barriers and QM-MM interaction energies converge with a LREC cutoff between 20 and 25 Å, in agreement with our previous results. Additionally, the LREC approach for the QM-MM interactions can be smoothly combined with standard shifting or Ewald summation methods in the MM calculations. We recommend the use of QM(LREC)/MM(PME), where the QM region is treated with LREC and the MM region is treated with particle mesh Ewald (PME) summation. This combination is an excellent compromise between simplicity, speed, and accuracy for large QM/MM simulations.
Collapse
Affiliation(s)
- Eric G Kratz
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Robert E Duke
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - G Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| |
Collapse
|
129
|
Lin D. Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors. J Chem Phys 2016; 143:114115. [PMID: 26395695 DOI: 10.1063/1.4930984] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Accurate representation of intermolecular forces has been the central task of classical atomic simulations, known as molecular mechanics. Recent advancements in molecular mechanics models have put forward the explicit representation of permanent and/or induced electric multipole (EMP) moments. The formulas developed so far to calculate EMP interactions tend to have complicated expressions, especially in Cartesian coordinates, which can only be applied to a specific kernel potential function. For example, one needs to develop a new formula each time a new kernel function is encountered. The complication of these formalisms arises from an intriguing and yet obscured mathematical relation between the kernel functions and the gradient operators. Here, I uncover this relation via rigorous derivation and find that the formula to calculate EMP interactions is basically invariant to the potential kernel functions as long as they are of the form f(r), i.e., any Green's function that depends on inter-particle distance. I provide an algorithm for efficient evaluation of EMP interaction energies, forces, and torques for any kernel f(r) up to any arbitrary rank of EMP moments in Cartesian coordinates. The working equations of this algorithm are essentially the same for any kernel f(r). Recently, a few recursive algorithms were proposed to calculate EMP interactions. Depending on the kernel functions, the algorithm here is about 4-16 times faster than these algorithms in terms of the required number of floating point operations and is much more memory efficient. I show that it is even faster than a theoretically ideal recursion scheme, i.e., one that requires 1 floating point multiplication and 1 addition per recursion step. This algorithm has a compact vector-based expression that is optimal for computer programming. The Cartesian nature of this algorithm makes it fit easily into modern molecular simulation packages as compared with spherical coordinate-based algorithms. A software library based on this algorithm has been implemented in C++11 and has been released.
Collapse
Affiliation(s)
- Dejun Lin
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| |
Collapse
|
130
|
Bojarowski SA, Kumar P, Dominiak PM. A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation. Chemphyschem 2016; 17:2455-60. [PMID: 27166026 DOI: 10.1002/cphc.201600390] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 12/23/2022]
Abstract
To compensate for the lack of the explicit treatment of charge penetration in classical force fields, we propose a new charge-distribution model based on a promolecule augmented with point charges (aug-PROmol). It relies on a superposition of spherical atomic electron densities obtained for each chemical element from SCF energy optimized atomic orbitals. Atomic densities are further rescaled by partial point charges computed from fits to the molecular electrostatic potential. Aug-PROmol was tested on the S66 benchmark dataset extended to nonequilibrium geometries (J. Chem. Theory Comput., 2011, 7, 3466). The model does not need any additional parametrization other than point charges. Despite its simplicity, aug-PROmol approximates the electrostatic energy with good agreement (RMSE=0.76 kcal mol(-1) to DFT-SAPT with B3LYP/aug-cc-pVTZ).
Collapse
Affiliation(s)
- Sławomir A Bojarowski
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Prashant Kumar
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland
| | - Paulina M Dominiak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089, Warszawa, Poland.
| |
Collapse
|
131
|
Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal JP. Polarizable molecular dynamics in a polarizable continuum solvent. J Chem Theory Comput 2016; 11:623-34. [PMID: 26516318 DOI: 10.1021/ct500998q] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-term energy conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
Collapse
Affiliation(s)
- Filippo Lipparini
- UniversitéPierre et Marie Curie−Paris 06 (UPMC), UMR 7598, Laboratoire Jacques-Louis Lions, Sorbonne Universités, F-75005, Paris, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
132
|
Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium simulations of thermally induced electric fields in water. J Chem Phys 2016; 144:224102. [DOI: 10.1063/1.4953036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- P. Wirnsberger
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - D. Fijan
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - A. Šarić
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - M. Neumann
- Faculty of Physics, University of Vienna, 1090 Vienna, Austria
| | - C. Dellago
- Faculty of Physics, University of Vienna, 1090 Vienna, Austria
| | - D. Frenkel
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
133
|
Giese TJ, York DM. Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation. J Chem Theory Comput 2016; 12:2611-32. [PMID: 27171914 DOI: 10.1021/acs.jctc.6b00198] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed.
Collapse
Affiliation(s)
- Timothy J Giese
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8087, United States
| | - Darrin M York
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854-8087, United States
| |
Collapse
|
134
|
Perilla JR, Hadden JA, Goh BC, Mayne CG, Schulten K. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets. J Phys Chem Lett 2016; 7:1836-44. [PMID: 27128262 PMCID: PMC4876486 DOI: 10.1021/acs.jpclett.6b00517] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid-protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid-drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.
Collapse
Affiliation(s)
- Juan R. Perilla
- Beckman Institute, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- E-mail: (J.R.P.)
| | - Jodi A. Hadden
- Beckman Institute, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Boon Chong Goh
- Beckman Institute, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Christopher G. Mayne
- Beckman Institute, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Klaus Schulten
- Beckman Institute, and Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- E-mail: (K.S.)
| |
Collapse
|
135
|
Simmonett AC, Pickard FC, Shao Y, Cheatham TE, Brooks BR. Efficient treatment of induced dipoles. J Chem Phys 2016; 143:074115. [PMID: 26298123 DOI: 10.1063/1.4928530] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most existing treatments of induced dipoles in polarizable molecular mechanics force field calculations use either the self-consistent variational method, which is solved iteratively, or the "direct" approximation that is non-iterative as a result of neglecting coupling between induced dipoles. The variational method is usually implemented using assumptions that are only strictly valid under tight convergence of the induced dipoles, which can be computationally demanding to enforce. In this work, we discuss the nature of the errors that result from insufficient convergence and suggest a strategy that avoids such problems. Using perturbation theory to reintroduce the mutual coupling into the direct algorithm, we present a computationally efficient method that combines the precision of the direct approach with the accuracy of the variational approach. By analyzing the convergence of this perturbation series, we derive a simple extrapolation formula that delivers a very accurate approximation to the infinite order solution at the cost of only a few iterations. We refer to the new method as extrapolated perturbation theory. Finally, we draw connections to our previously published permanent multipole algorithm to develop an efficient implementation of the electric field and Thole terms and also derive some necessary, but not sufficient, criteria that force field parameters must obey.
Collapse
Affiliation(s)
- Andrew C Simmonett
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yihan Shao
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
136
|
Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal JP, Cisneros GA. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. J Comput Chem 2016; 37:1019-29. [PMID: 26781073 PMCID: PMC4808410 DOI: 10.1002/jcc.24295] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 12/23/2022]
Abstract
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.
Collapse
|
137
|
Rossi G, Monticelli L. Gold nanoparticles in model biological membranes: A computational perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2380-2389. [PMID: 27060434 DOI: 10.1016/j.bbamem.2016.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 01/15/2023]
Abstract
The electronic, optical, catalytic, and magnetic properties of metal nanoparticles (NPs) make them extremely interesting for biomedical applications. In this rapidly moving field, monolayer-protected gold nanoparticles emerge both as a reference system and as promising candidates for drug and gene delivery, photothermal treatment, and imaging applications. Despite the technological relevance, there is still poor understanding of the molecular processes driving the interactions of metal nanoparticles with cells, and with cell membranes in particular. In this paper we review molecular-level computational studies of the interaction between monolayer-protected gold NPs and model lipid membranes. Our review comprises a brief description of the most relevant experimental results in this field and of the questions they raised, followed by a description of the computational achievements reported so far. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Collapse
Affiliation(s)
- Giulia Rossi
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy.
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS UMR 5086, 7 Passage du Vercors, 69007 Lyon, France.
| |
Collapse
|
138
|
Wang H, Nakamura H, Fukuda I. A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system. J Chem Phys 2016; 144:114503. [DOI: 10.1063/1.4943956] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Han Wang
- CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, 100088 Beijing, China and Zuse Institute Berlin (ZIB), Berlin, Germany
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ikuo Fukuda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| |
Collapse
|
139
|
Zhang L, Bennett WFD, Zheng T, Ouyang PK, Ouyang X, Qiu X, Luo A, Karttunen M, Chen P. Effect of Cholesterol on Cellular Uptake of Cancer Drugs Pirarubicin and Ellipticine. J Phys Chem B 2016; 120:3148-56. [PMID: 26937690 DOI: 10.1021/acs.jpcb.5b12337] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lei Zhang
- Biological
and Pharmaceutical Engineering, Nanjing Technology University, 30 Puzhu Road South, Nanjing, Jiangsu, China, 211816
- Department
of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1
| | - W. F. Drew Bennett
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tao Zheng
- Biological
and Pharmaceutical Engineering, Nanjing Technology University, 30 Puzhu Road South, Nanjing, Jiangsu, China, 211816
| | - Ping-Kai Ouyang
- Biological
and Pharmaceutical Engineering, Nanjing Technology University, 30 Puzhu Road South, Nanjing, Jiangsu, China, 211816
| | - Xinping Ouyang
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, P.R. China, 510640
| | - Xueqing Qiu
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, P.R. China, 510640
| | - Anqi Luo
- Department
of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems, Eindhoven University of Technology, MetaForum, 5600 MB Eindhoven, The Netherlands
| | - P. Chen
- Biological
and Pharmaceutical Engineering, Nanjing Technology University, 30 Puzhu Road South, Nanjing, Jiangsu, China, 211816
- Department
of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1
| |
Collapse
|
140
|
Narth C, Lagardère L, Polack É, Gresh N, Wang Q, Bell DR, Rackers JA, Ponder JW, Ren PY, Piquemal JP. Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles. J Comput Chem 2016; 37:494-506. [PMID: 26814845 PMCID: PMC4730919 DOI: 10.1002/jcc.24257] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/02/2015] [Accepted: 10/21/2015] [Indexed: 12/25/2022]
Abstract
We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions.
Collapse
Affiliation(s)
- Christophe Narth
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
| | - Louis Lagardère
- UPMC Univ. Paris 06, Institut du Calcul et de la Simulation, F-75005, Paris, France
| | - Étienne Polack
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- UPMC Univ. Paris 06, UMR 7598, Laboratoire Jacques-Louis Lions, F-75005, Paris, France
| | - Nohad Gresh
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
- Chemistry and Biology Nucleo(s)tides and immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomédicale, Paris 75006, France
| | - Qiantao Wang
- Department of Biomedical Engineering, The University of Texas at Austin, Texas 78712
| | - David R. Bell
- Department of Biomedical Engineering, The University of Texas at Austin, Texas 78712
| | - Joshua A. Rackers
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Jay W. Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Pengyu Y. Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Texas 78712
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, F-75005, Paris, France
| |
Collapse
|
141
|
The good, the bad and the user in soft matter simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2529-2538. [PMID: 26862882 DOI: 10.1016/j.bbamem.2016.02.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 11/21/2022]
Abstract
Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Collapse
|
142
|
Cino EA, Choy WY, Karttunen M. Characterization of the Free State Ensemble of the CoRNR Box Motif by Molecular Dynamics Simulations. J Phys Chem B 2016; 120:1060-8. [DOI: 10.1021/acs.jpcb.5b11565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Elio A. Cino
- Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Wing-Yiu Choy
- Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & the Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum, Eindhoven 5600 MB, The Netherlands
| |
Collapse
|
143
|
Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
Collapse
Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| |
Collapse
|
144
|
Wang B, Truhlar DG. Screened Electrostatic Interactions in Molecular Mechanics. J Chem Theory Comput 2015; 10:4480-7. [PMID: 26588144 DOI: 10.1021/ct5005142] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal/mol. We could have decreased the average errors further, but at the cost of sometimes significantly overestimating the screening; instead we chose a more conservative (safer) parametrization that systematically underestimates the screening (which by definition means it improves over point charges) and only occasionally overestimates it. Despite this conservative choice, we find that the screened MM method is even more accurate for the electrostatics than unscreened QM/MM calculations. This new method is easy to implement in any MM program, and it can be used to develop more physical force fields for molecular simulations.
Collapse
Affiliation(s)
- Bo Wang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| |
Collapse
|
145
|
Do TN, Choy WY, Karttunen M. Accelerating the Conformational Sampling of Intrinsically Disordered Proteins. J Chem Theory Comput 2015; 10:5081-94. [PMID: 26584388 DOI: 10.1021/ct5004803] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) are a class of proteins lacking a well-defined secondary structure. Instead, they are able to attain multiple conformations, bind to multiple targets, and respond to changes in their surroundings. Functionally, IDPs have been associated with molecular recognition, cell regulation, and signal transduction. The dynamic conformational ensemble of IDPs is highly environmental and binding partner dependent, rendering the characterization of IDPs extremely challenging. Here, we compare the sampling efficiencies of conventional molecular dynamics (MD), well-tempered metadynamics (WT-META), and bias-exchange metadynamics (BE-META). The total simulation time was over 10 μs, and a 20-mer peptide derived from the Neh2 domain of the Nuclear factor erythroid 2-related factor 2 (Nrf2) protein was simulated. BE-META, with a neutral replica and seven biased replicas employing a set of seven relevant collective variables (CVs), provided the most reliable and efficient sampling. Finally, we propose a free-energy reconstruction method based on the probability distribution of the secondary structure contents. This postprocessing analysis confirms the presence of not only the β-hairpin conformation of the free Neh2 peptide but also its rare bound-state-like conformation, both of that have been experimentally observed. In addition, our simulations also predict other possible conformations to be verified with future experiments.
Collapse
Affiliation(s)
- Trang Nhu Do
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, University of Western Ontario , 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Mikko Karttunen
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo , 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
146
|
Hagler AT. Quantum Derivative Fitting and Biomolecular Force Fields: Functional Form, Coupling Terms, Charge Flux, Nonbond Anharmonicity, and Individual Dihedral Potentials. J Chem Theory Comput 2015; 11:5555-72. [DOI: 10.1021/acs.jctc.5b00666] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- A. T. Hagler
- Department of Chemistry University of Massachusetts, Amherst, Massachusetts 01003, United States
- Shifa Biopharm, Shifa Biomedical Corporation, Malvern, Pennsylvania 19355, United States
| |
Collapse
|
147
|
Lorenzen K, Mathias G, Tavan P. Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions. J Chem Phys 2015; 143:184114. [PMID: 26567653 DOI: 10.1063/1.4935514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved-up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.
Collapse
Affiliation(s)
- Konstantin Lorenzen
- Lehrstuhl für BioMolekulare Optik, Ludig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Gerald Mathias
- Lehrstuhl für BioMolekulare Optik, Ludig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl für BioMolekulare Optik, Ludig-Maximilians Universität München, Oettingenstr. 67, 80538 München, Germany
| |
Collapse
|
148
|
Ojeda-May P, Pu J. Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations. J Chem Phys 2015; 143:174111. [PMID: 26547162 PMCID: PMC4636498 DOI: 10.1063/1.4934880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 10/19/2015] [Indexed: 11/14/2022] Open
Abstract
The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i.e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions.
Collapse
Affiliation(s)
- Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, USA
| |
Collapse
|
149
|
Titantah JT, Karttunen M. Hydrophobicity: effect of density and order on water's rotational slowing down. SOFT MATTER 2015; 11:7977-7985. [PMID: 26327528 DOI: 10.1039/c5sm00930h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ab initio molecular dynamics (AIMD) simulations of over 4.5 ns were performed in the temperature range of T = 260-350 K with van der Waals corrections to investigate the relationship between local water density and tetrahedral order in bulk water and in the presence of a hydrophobe, tetramethylurea (TMU). We demonstrate that in bulk water, defects consisting of 5- and higher coordinated water are a major contributor to dynamics. Close to a hydrophobe, 3-coordinated defects take over. The co-existence of these defects gives rise to very different local densities. We propose that the slowing down of rotational motion close to a hydrophobe is induced by an interplay between density and order with the slowing down decreasing in the following order: (i) low-density ordered-water, (ii) normal-density ordered-water, (iii) high-density ordered-water and (iv) disordered-water. The proportions of these water environments vary with temperature. These local environments also support the idea of water's polymorphism, i.e., the existence of the high- and low-density states in supercooled water.
Collapse
Affiliation(s)
- John Tatini Titantah
- Department of Applied Mathematics, University of Western Ontario, 1151 Richmond Street North, London, Ontario, Canada N6A 5B7
| | | |
Collapse
|
150
|
Antila HS, Tassel PRV, Sammalkorpi M. Ewald Electrostatics for Mixtures of Point and Continuous Line Charges. J Phys Chem B 2015; 119:13218-26. [DOI: 10.1021/acs.jpcb.5b07637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hanne S. Antila
- Department
of Chemistry, Aalto University, 00076 Aalto, Finland
| | - Paul R. Van Tassel
- Department of Chemical & Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | | |
Collapse
|