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Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024; 161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program is designed to treat short-range and long-range interactions through user-specified combinations of electrostatic and mechanical embedding procedures within periodic simulation domains, providing necessary interfaces to external quantum chemistry and molecular dynamics software. To enable direct embedding of long-range electrostatics in periodic systems, we have derived and implemented force terms for our previously described QM/MM/PME approach [Pederson and McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with external software packages Psi4 and OpenMM is facilitated through Python application programming interfaces (APIs). The core library contains basic utilities for running QM/MM molecular dynamics simulations, and plug-in entry-points are provided for users to implement custom energy/force calculation and integration routines, within an extensible architecture. The user interacts with PyDFT-QMMM primarily through its Python API, allowing for complex workflow development with Python scripting, for example, interfacing with PLUMED for free energy simulations. We provide benchmarks of forces and energy conservation for the QM/MM/PME and alternative QM/MM electrostatic embedding approaches. We further demonstrate a simple example use case for water solute in a water solvent system, for which radial distribution functions are computed from 100 ps QM/MM simulations; in this example, we highlight how the solvation structure is sensitive to different basis-set choices due to under- or over-polarization of the QM water molecule's electron density.
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Affiliation(s)
- John P Pederson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Jesse G McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Nocito D, Beran GJO. Averaged Condensed Phase Model for Simulating Molecules in Complex Environments. J Chem Theory Comput 2017; 13:1117-1129. [PMID: 28170251 DOI: 10.1021/acs.jctc.6b00890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The need for configurational sampling dramatically increases the cost of combined quantum mechanics/molecular mechanics (QM/MM) simulations of chemical processes in solution. We developed an averaged condensed phase environment (ACPE) model that constructs an effective polarizable environment directly from explicitly sampled molecular dynamics configurations via the K-means++ algorithm and a mathematically rigorous translation of the molecular mechanics parameters. The model captures detailed heterogeneous features in the environment that may be difficult to describe using a conventional polarizable continuum model. Instead of performing repeated QM/MM calculations for each new configuration of the environment, the ACPE approach allows one to perform a single QM calculation on an averaged configuration. Here, we demonstrate the model by computing electronic excitation energies for several small molecules in solution. The ACPE model predicts the excitation energies in excellent agreement with conventional configurational averaging yet with orders of magnitude of reduction in the computational cost.
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Affiliation(s)
- Dominique Nocito
- Department of Chemistry, University of California , Riverside, California 92521, United States
| | - Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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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.
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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
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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.
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Janowski T, Wolinski K, Pulay P. Efficient calculation of the density response function from generalized polarizabilities. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1761-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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König G, Mei Y, Pickard FC, Simmonett AC, Miller BT, Herbert JM, Woodcock HL, Brooks BR, Shao Y. Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method. J Chem Theory Comput 2015; 12:332-44. [PMID: 26613419 DOI: 10.1021/acs.jctc.5b00874] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10-0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study.
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Affiliation(s)
- Gerhard König
- 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 and Department of Physics and Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China 200062
| | - 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
| | - 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
| | - Benjamin T Miller
- 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
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, 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
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Sodt AJ, Mei Y, König G, Tao P, Steele RP, Brooks BR, Shao Y. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. J Phys Chem A 2014; 119:1511-23. [PMID: 25321186 PMCID: PMC4353191 DOI: 10.1021/jp5072296] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
combined quantum mechanical/molecular mechanical (QM/MM) free
energy calculations, it is often advantageous to have a frozen geometry
for the quantum mechanical (QM) region. For such multiple-environment
single-system (MESS) cases, two schemes are proposed here for estimating
the polarization energy: the first scheme, termed MESS-E, involves
a Roothaan step extrapolation of the self-consistent field (SCF) energy;
whereas the other scheme, termed MESS-H, employs a Newton–Raphson
correction using an approximate inverse electronic Hessian of the
QM region (which is constructed only once). Both schemes are extremely
efficient, because the expensive Fock updates and SCF iterations in
standard QM/MM calculations are completely avoided at each configuration.
They produce reasonably accurate QM/MM polarization energies: MESS-E
can predict the polarization energy within 0.25 kcal/mol in terms
of the mean signed error for two of our test cases, solvated methanol
and solvated β-alanine, using the M06-2X or ωB97X-D functionals;
MESS-H can reproduce the polarization energy within 0.2 kcal/mol for
these two cases and for the oxyluciferin–luciferase complex,
if the approximate inverse electronic Hessians are constructed with
sufficient accuracy.
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Affiliation(s)
- Alexander J Sodt
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
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Wu X, Wu G. An adaptive immune optimization algorithm with dynamic lattice searching operation for fast optimization of atomic clusters. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Janowski T. Near Equivalence of Intrinsic Atomic Orbitals and Quasiatomic Orbitals. J Chem Theory Comput 2014; 10:3085-91. [DOI: 10.1021/ct500245f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomasz Janowski
- Department
of Chemistry and
Biochemistry Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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Shiga M, Masia M. Boundary based on exchange symmetry theory for multilevel simulations. II. Multiple time scale approach. J Chem Phys 2013; 139:144103. [DOI: 10.1063/1.4823729] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pulay P. Analytical derivatives, forces, force constants, molecular geometries, and related response properties in electronic structure theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1171] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Peter Pulay
- Department of Chemistry and Biochemistry University of Arkansas Fayetteville Arkansas USA
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Theel KL, Wen S, Beran GJO. Communication: Constructing an implicit quantum mechanical/molecular mechanics solvent model by coarse-graining explicit solvent. J Chem Phys 2013; 139:081103. [DOI: 10.1063/1.4819774] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Shiga M, Masia M. Boundary based on exchange symmetry theory for multilevel simulations. I. Basic theory. J Chem Phys 2013; 139:044120. [DOI: 10.1063/1.4816629] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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