1
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Koskin V, Kells A, Clayton J, Hartmann AK, Annibale A, Rosta E. Variational kinetic clustering of complex networks. J Chem Phys 2023; 158:104112. [PMID: 36922127 DOI: 10.1063/5.0105099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Efficiently identifying the most important communities and key transition nodes in weighted and unweighted networks is a prevalent problem in a wide range of disciplines. Here, we focus on the optimal clustering using variational kinetic parameters, linked to Markov processes defined on the underlying networks, namely, the slowest relaxation time and the Kemeny constant. We derive novel relations in terms of mean first passage times for optimizing clustering via the Kemeny constant and show that the optimal clustering boundaries have equal round-trip times to the clusters they separate. We also propose an efficient method that first projects the network nodes onto a 1D reaction coordinate and subsequently performs a variational boundary search using a parallel tempering algorithm, where the variational kinetic parameters act as an energy function to be extremized. We find that maximization of the Kemeny constant is effective in detecting communities, while the slowest relaxation time allows for detection of transition nodes. We demonstrate the validity of our method on several test systems, including synthetic networks generated from the stochastic block model and real world networks (Santa Fe Institute collaboration network, a network of co-purchased political books, and a street network of multiple cities in Luxembourg). Our approach is compared with existing clustering algorithms based on modularity and the robust Perron cluster analysis, and the identified transition nodes are compared with different notions of node centrality.
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Affiliation(s)
- Vladimir Koskin
- Department of Chemistry, King's College London, SE1 1DB London, United Kingdom
| | - Adam Kells
- Department of Chemistry, King's College London, SE1 1DB London, United Kingdom
| | - Joe Clayton
- Department of Physics and Astronomy, University College London, WC1E 6BT London, United Kingdom
| | | | - Alessia Annibale
- Department of Mathematics, King's College London, SE11 6NJ London, United Kingdom
| | - Edina Rosta
- Department of Physics and Astronomy, University College London, WC1E 6BT London, United Kingdom
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2
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Kamenik AS, Linker SM, Riniker S. Enhanced sampling without borders: on global biasing functions and how to reweight them. Phys Chem Chem Phys 2022; 24:1225-1236. [PMID: 34935813 PMCID: PMC8768491 DOI: 10.1039/d1cp04809k] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 12/17/2022]
Abstract
Molecular dynamics (MD) simulations are a powerful tool to follow the time evolution of biomolecular motions in atomistic resolution. However, the high computational demand of these simulations limits the timescales of motions that can be observed. To resolve this issue, so called enhanced sampling techniques are developed, which extend conventional MD algorithms to speed up the simulation process. Here, we focus on techniques that apply global biasing functions. We provide a broad overview of established enhanced sampling methods and promising new advances. As the ultimate goal is to retrieve unbiased information from biased ensembles, we also discuss benefits and limitations of common reweighting schemes. In addition to concisely summarizing critical assumptions and implications, we highlight the general application opportunities as well as uncertainties of global enhanced sampling.
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Affiliation(s)
- Anna S Kamenik
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Stephanie M Linker
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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3
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Shu Z, Wu M, Liao J, Chen C. FSATOOL 2.0: An integrated molecular dynamics simulation and trajectory data analysis program. J Comput Chem 2021; 43:215-224. [PMID: 34751974 DOI: 10.1002/jcc.26772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022]
Abstract
Molecular dynamics simulation is important in the computational study of the biomolecules. In this paper, we upgrade our previous FSATOOL to version 2.0. It is no longer a plugin as before. Besides the existed enhanced sampling and Markov state model analysis module, FSATOOL 2.0 has three new features now. First, it contains a molecular dynamics simulation engine on both CPU and GPU device. The engine works with an embedded enhanced sampling module. Second, it can do the free energy calculation by various practical methods, including the weighted histogram analysis method and Gaussian mixture model. Third, it has many subroutines to process the trajectory data, such as principal component analysis, time-structure based independent component analysis, contact analysis, and Φ-value analysis. Most importantly, all these calculations are integrated into one package. The trajectory data format is compatible with all the modules. With a proper input parameter file, users can do the molecular dynamics simulation and data analysis work by only a few simplified commands. The capabilities and theoretical backgrounds of FSATOOL 2.0 are introduced in the paper.
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Affiliation(s)
- Zirui Shu
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mincong Wu
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jun Liao
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
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4
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Faizi F, Buigues PJ, Deligiannidis G, Rosta E. Simulated tempering with irreversible Gibbs sampling techniques. J Chem Phys 2020; 153:214111. [PMID: 33291930 DOI: 10.1063/5.0025775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present here two novel algorithms for simulated tempering simulations, which break the detailed balance condition (DBC) but satisfy the skewed detailed balance to ensure invariance of the target distribution. The irreversible methods we present here are based on Gibbs sampling and concern breaking DBC at the update scheme of the temperature swaps. We utilize three systems as a test bed for our methods: a Markov chain Monte Carlo simulation on a simple system described by a one-dimensional double well potential, the Ising model, and molecular dynamics simulations on alanine pentapeptide (ALA5). The relaxation times of inverse temperature, magnetic susceptibility, and energy density for the Ising model indicate clear gains in sampling efficiency over conventional Gibbs sampling techniques with DBC and also over the conventionally used simulated tempering with the Metropolis-Hastings (MH) scheme. Simulations on ALA5 with a large number of temperatures indicate distinct gains in mixing times for inverse temperature and consequently the energy of the system compared to conventional MH. With no additional computational overhead, our methods were found to be more efficient alternatives to the conventionally used simulated tempering methods with DBC. Our algorithms should be particularly advantageous in simulations of large systems with many temperature ladders, as our algorithms showed a more favorable constant scaling in Ising spin systems as compared with both reversible and irreversible MH algorithms. In future applications, our irreversible methods can also be easily tailored to utilize a given dynamical variable other than temperature to flatten rugged free energy landscapes.
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Affiliation(s)
- Fahim Faizi
- Department of Mathematics, King's College London, Strand, WC2R 2LS London, United Kingdom
| | - Pedro J Buigues
- Department of Chemistry, King's College London, 7 Trinity Street, SE1 1DB London, United Kingdom
| | - George Deligiannidis
- Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, United Kingdom
| | - Edina Rosta
- Department of Chemistry, King's College London, 7 Trinity Street, SE1 1DB London, United Kingdom
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5
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Xia J, Flynn W, Gallicchio E, Uplinger K, Armstrong JD, Forli S, Olson AJ, Levy RM. Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. J Chem Inf Model 2019; 59:1382-1397. [PMID: 30758197 PMCID: PMC6496938 DOI: 10.1021/acs.jcim.8b00817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To perform massive-scale replica exchange molecular dynamics (REMD) simulations for calculating binding free energies of protein-ligand complexes, we implemented the asynchronous replica exchange (AsyncRE) framework of the binding energy distribution analysis method (BEDAM) in implicit solvent on the IBM World Community Grid (WCG) and optimized the simulation parameters to reduce the overhead and improve the prediction power of the WCG AsyncRE simulations. We also performed the first massive-scale binding free energy calculations using the WCG distributed computing grid and 301 ligands from the SAMPL4 challenge for large-scale binding free energy predictions of HIV-1 integrase complexes. In total there are ∼10000 simulated complexes, ∼1 million replicas, and ∼2000 μs of aggregated MD simulations. Running AsyncRE MD simulations on the WCG requires accepting a trade-off between the number of replicas that can be run (breadth) and the number of full RE cycles that can be completed per replica (depth). As compared with synchronous Replica Exchange (SyncRE) running on tightly coupled clusters like XSEDE, on the WCG many more replicas can be launched simultaneously on heterogeneous distributed hardware, but each full RE cycle requires more overhead. We compared the WCG results with that from AutoDock and more advanced RE simulations including the use of flattening potentials to accelerate sampling of selected degrees of freedom of ligands and/or receptors related to slow dynamics due to high energy barriers. We propose a suitable strategy of RE simulations to refine high throughput docking results which can be matched to corresponding computing resources: from HPC clusters, to small or medium-size distributed campus grids, and finally to massive-scale computing networks including millions of CPUs like the resources available on the WCG.
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Affiliation(s)
- Junchao Xia
- Center for Biophysics and Computational Biology and Department of Physics , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - William Flynn
- Center for Biophysics and Computational Biology and Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Emilio Gallicchio
- Department of Chemistry , CUNY Brooklyn College , Brooklyn , New York 11210 , United States
| | - Keith Uplinger
- IBM WCG Team, 1177 South Belt Line Road , Coppell , Texas 75019 , United States
| | - Jonathan D Armstrong
- IBM WCG Team, 11400 Burnet Road , 0453B129, Austin , Texas 78758 , United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037-1000 , United States
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037-1000 , United States
| | - Ronald M Levy
- Center for Biophysics and Computational Biology and Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
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6
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Wingbermühle S, Schäfer LV. On Obtaining Boltzmann-Distributed Configurational Ensembles from Expanded Ensemble Simulations with Fast State Mixing. J Chem Theory Comput 2019; 15:2774-2779. [DOI: 10.1021/acs.jctc.9b00100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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7
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Leahy CT, Kells A, Hummer G, Buchete NV, Rosta E. Peptide dimerization-dissociation rates from replica exchange molecular dynamics. J Chem Phys 2018; 147:152725. [PMID: 29055328 DOI: 10.1063/1.5004774] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We show how accurate rates of formation and dissociation of peptide dimers can be calculated using direct transition counting (DTC) from replica-exchange molecular dynamics (REMD) simulations. First, continuous trajectories corresponding to system replicas evolving at different temperatures are used to assign conformational states. Second, we analyze the entire REMD data to calculate the corresponding rates at each temperature directly from the number of transition counts. Finally, we compare the kinetics extracted directly, using the DTC method, with indirect estimations based on trajectory likelihood maximization using short-time propagators and on decay rates of state autocorrelation functions. For systems with relatively low-dimensional intrinsic conformational dynamics, the DTC method is simple to implement and leads to accurate temperature-dependent rates. We apply the DTC rate-extraction method to all-atom REMD simulations of dimerization of amyloid-forming NNQQ tetrapetides in explicit water. In an assessment of the REMD sampling efficiency with respect to standard MD, we find a gain of more than a factor of two at the lowest temperature.
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Affiliation(s)
- Cathal T Leahy
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Adam Kells
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | | | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
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8
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Chen C. Constructing a multidimensional free energy surface like a spider weaving a web. J Comput Chem 2017; 38:2298-2306. [PMID: 28718973 DOI: 10.1002/jcc.24881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/20/2017] [Accepted: 06/22/2017] [Indexed: 01/13/2023]
Abstract
Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast-growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow-growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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9
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Tan Z, Xia J, Zhang BW, Levy RM. Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation. J Chem Phys 2016; 144:034107. [PMID: 26801020 DOI: 10.1063/1.4939768] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The weighted histogram analysis method (WHAM) including its binless extension has been developed independently in several different contexts, and widely used in chemistry, physics, and statistics, for computing free energies and expectations from multiple ensembles. However, this method, while statistically efficient, is computationally costly or even infeasible when a large number, hundreds or more, of distributions are studied. We develop a locally WHAM (local WHAM) from the perspective of simulations of simulations (SOS), using generalized serial tempering (GST) to resample simulated data from multiple ensembles. The local WHAM equations based on one jump attempt per GST cycle can be solved by optimization algorithms orders of magnitude faster than standard implementations of global WHAM, but yield similarly accurate estimates of free energies to global WHAM estimates. Moreover, we propose an adaptive SOS procedure for solving local WHAM equations stochastically when multiple jump attempts are performed per GST cycle. Such a stochastic procedure can lead to more accurate estimates of equilibrium distributions than local WHAM with one jump attempt per cycle. The proposed methods are broadly applicable when the original data to be "WHAMMED" are obtained properly by any sampling algorithm including serial tempering and parallel tempering (replica exchange). To illustrate the methods, we estimated absolute binding free energies and binding energy distributions using the binding energy distribution analysis method from one and two dimensional replica exchange molecular dynamics simulations for the beta-cyclodextrin-heptanoate host-guest system. In addition to the computational advantage of handling large datasets, our two dimensional WHAM analysis also demonstrates that accurate results similar to those from well-converged data can be obtained from simulations for which sampling is limited and not fully equilibrated.
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Affiliation(s)
- Zhiqiang Tan
- Department of Statistics, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Junchao Xia
- Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Bin W Zhang
- Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
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10
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Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV. Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. J Phys Chem Lett 2016; 7:2676-2682. [PMID: 27323250 DOI: 10.1021/acs.jpclett.6b00518] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We characterize the kinetics of dimer formation of the short amyloid microcrystal-forming tetrapeptides NNQQ by constructing coarse master equations for the conformational dynamics of the system, using temperature replica-exchange molecular dynamics (REMD) simulations. We minimize the effects of Kramers-type recrossings by assigning conformational states based on their sequential time evolution. Transition rates are further estimated from short-time state propagators by maximizing the likelihood that the extracted rates agree with the observed atomistic trajectories without any a priori assumptions about their temperature dependence. Here, we evaluate the rates for both continuous replica trajectories that visit different temperatures and for discontinuous data corresponding to each REMD temperature. While the binding-unbinding kinetic process is clearly Markovian, the conformational dynamics of the bound NNQQ dimer has a complex character. Our kinetic analysis allows us to discriminate between short-lived encounter pairs and strongly bound conformational states. The conformational dynamics of NNQQ dimers supports a kinetically driven aggregation mechanism, in agreement with the polymorphic character reported for amyloid aggregates such as microcrystals and fibrils.
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Affiliation(s)
- Cathal T Leahy
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
| | - Ronan D Murphy
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Edina Rosta
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
| | - Nicolae-Viorel Buchete
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
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11
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Hoang Viet M, Derreumaux P, Nguyen PH. Communication: Multiple atomistic force fields in a single enhanced sampling simulation. J Chem Phys 2016; 143:021101. [PMID: 26178083 DOI: 10.1063/1.4926535] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.
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Affiliation(s)
- Man Hoang Viet
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, USA
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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12
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Chen C, Huang Y. Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method. J Comput Chem 2016; 37:1565-75. [DOI: 10.1002/jcc.24371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modelling Group, School of Physics; Huazhong University of Science and Technology; Wuhan Hubei 430074 China
| | - Yanzhao Huang
- Biomolecular Physics and Modelling Group, School of Physics; Huazhong University of Science and Technology; Wuhan Hubei 430074 China
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13
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Pan AC, Weinreich TM, Piana S, Shaw DE. Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems. J Chem Theory Comput 2016; 12:1360-7. [PMID: 26866996 DOI: 10.1021/acs.jctc.5b00913] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics (MD) simulations can describe protein motions in atomic detail, but transitions between protein conformational states sometimes take place on time scales that are infeasible or very expensive to reach by direct simulation. Enhanced sampling methods, the aim of which is to increase the sampling efficiency of MD simulations, have thus been extensively employed. The effectiveness of such methods when applied to complex biological systems like proteins, however, has been difficult to establish because even enhanced sampling simulations of such systems do not typically reach time scales at which convergence is extensive enough to reliably quantify sampling efficiency. Here, we obtain sufficiently converged simulations of three proteins to evaluate the performance of simulated tempering, a member of a widely used class of enhanced sampling methods that use elevated temperature to accelerate sampling. Simulated tempering simulations with individual lengths of up to 100 μs were compared to (previously published) conventional MD simulations with individual lengths of up to 1 ms. With two proteins, BPTI and ubiquitin, we evaluated the efficiency of sampling of conformational states near the native state, and for the third, the villin headpiece, we examined the rate of folding and unfolding. Our comparisons demonstrate that simulated tempering can consistently achieve a substantial sampling speedup of an order of magnitude or more relative to conventional MD.
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Affiliation(s)
- Albert C Pan
- D. E. Shaw Research , New York, New York 10036, United States
| | | | - Stefano Piana
- D. E. Shaw Research , New York, New York 10036, United States
| | - David E Shaw
- D. E. Shaw Research , New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York 10032, United States
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14
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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.
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15
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Lenner N, Mathias G. Continuous Tempering Molecular Dynamics: A Deterministic Approach to Simulated Tempering. J Chem Theory Comput 2016; 12:486-98. [DOI: 10.1021/acs.jctc.5b00751] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicolas Lenner
- Lehrstuhl für BioMolekulare Optik, Ludwig−Maximilians Universität München, Oettingenstrasse 67, 80538 München, Germany
| | - Gerald Mathias
- Lehrstuhl für BioMolekulare Optik, Ludwig−Maximilians Universität München, Oettingenstrasse 67, 80538 München, Germany
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16
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Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z, Levy RM. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. J Comput Chem 2015; 36:1772-85. [PMID: 26149645 PMCID: PMC4512903 DOI: 10.1002/jcc.23996] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 01/25/2023]
Abstract
We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta-cyclodextrin-heptanoate host-guest system in the context of one- and two-dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (>picoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle.
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Affiliation(s)
- Junchao Xia
- Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122
| | - William F. Flynn
- Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122
- Department of Physics & Astronomy, Rutgers University, Piscataway, NJ 08854
| | | | - Bin W. Zhang
- Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122
| | - Peng He
- Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122
| | - Zhiqiang Tan
- Department of Statistics, Rutgers University, Piscataway, NJ 08854
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Department of Chemistry and Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122
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Luitz M, Bomblies R, Ostermeir K, Zacharias M. Exploring biomolecular dynamics and interactions using advanced sampling methods. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:323101. [PMID: 26194626 DOI: 10.1088/0953-8984/27/32/323101] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular dynamics (MD) and Monte Carlo (MC) simulations have emerged as a valuable tool to investigate statistical mechanics and kinetics of biomolecules and synthetic soft matter materials. However, major limitations for routine applications are due to the accuracy of the molecular mechanics force field and due to the maximum simulation time that can be achieved in current simulations studies. For improving the sampling a number of advanced sampling approaches have been designed in recent years. In particular, variants of the parallel tempering replica-exchange methodology are widely used in many simulation studies. Recent methodological advancements and a discussion of specific aims and advantages are given. This includes improved free energy simulation approaches and conformational search applications.
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Affiliation(s)
- Manuel Luitz
- Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748 Garching, Germany
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18
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Zhang T, Nguyen PH, Nasica-Labouze J, Mu Y, Derreumaux P. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J Phys Chem B 2015; 119:6941-51. [PMID: 25985144 DOI: 10.1021/acs.jpcb.5b03381] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Following a previous report on a coarse-grained protein model in implicit solvent, we applied simulated tempering (ST) with on-the-fly Helmholtz free energy (weight factors) determination to the folding or aggregation of seven proteins with the CHARMM, OPLS, and AMBER protein, and the SPC and TIP3P water force fields. For efficiency and reliability, we also performed replica exchange molecular dynamics (REMD) simulations on the alanine di- and deca-peptide, and the dimer of the Aβ16-22 Alzheimer's fragment, and used experimental data and previous simulation results on the chignolin, beta3s, Trp-cage, and WW domain peptides of 10-37 amino acids. The sampling with ST is found to be more efficient than with REMD for a much lower CPU cost. Starting from unfolded or extended conformations, the WW domain and the Trp-cage peptide fold to their NMR structures with a backbone RMSD of 2.0 and 1 Å. Remarkably, the ST simulation explores transient non-native topologies for Trp-cage that have been rarely discussed by other simulations. Our ST simulations also show that the CHARMM22* force field has limitations in describing accurately the beta3s peptide. Taken together, these results open the door to the study of the configurations of single proteins, protein aggregates, and any molecular systems at atomic details in explicit solvent using a single normal CPU. They also demonstrate that our ST scheme can be used with any force field ranging from quantum mechanics to coarse-grain and atomistic.
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Affiliation(s)
- Tong Zhang
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,§International School of Advanced Studies (SISSA), Via Bonomea, 265, 34126 Trieste, Italy
| | - Yuguang Mu
- ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.,∥Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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19
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Jo S, Chipot C, Roux B. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics. J Chem Theory Comput 2015; 11:2234-44. [DOI: 10.1021/ct501034w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sunhwan Jo
- Argonne
Leadership Computing Facility, Argonne National Laboratory, 9700 South
Cass Avenue, Building 240, Lemont, 60439 Illinois, United States
| | - Christophe Chipot
- Laboratoire
International Associé Centre National de la Recherche Scientifique
and University of Illinois at Urbana−Champaign, UMR 7565, Université de Lorraine, BP 70239, 54506 Vandœuvre-lès-Nancy, France
- Department
of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Research and Technology, University of Illinois at Urbana−Champaign, 405 North Mathews, Urbana, Illinois 61801, United States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, Gordon Center for Integrative
Science, University of Chicago, Chicago, Illinois 60637, United States
- Center
for
Nanoscale Materials, Argonne National Laboratory, 9700 South Cass Avenue, Building
440, Argonne, Illinois 60439, United States
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20
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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21
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Nguyen PH, Okamoto Y, Derreumaux P. Communication: Simulated tempering with fast on-the-fly weight determination. J Chem Phys 2013; 138:061102. [DOI: 10.1063/1.4792046] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:847-53. [PMID: 23298543 DOI: 10.1016/j.bbapap.2012.12.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/23/2012] [Accepted: 12/24/2012] [Indexed: 11/20/2022]
Abstract
Molecular dynamics (MD) simulations are ideally suited to investigate protein and peptide plasticity and flexibility simultaneously at high spatial (atomic) and high time resolution. However, the applicability is still limited by the force field accuracy and by the maximum simulation time that can be routinely achieved in current MD simulations. In order to improve the sampling the replica-exchange (REMD) methodology has become popular and is now the most widely applied advanced sampling approach. Many variants of the REMD method have been designed to reduce the computational demand or to enhance sampling along specific sets of conformational variables. An overview on recent methodological advances and discussion of specific aims and advantages of the approaches will be given. Applications in the area of free energy simulations and advanced sampling of intrinsically disordered peptides and proteins will also be discussed. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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23
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Fuller JC, Jackson RM, Shirts MR. Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities. J Phys Chem B 2012; 116:10856-69. [PMID: 22920218 DOI: 10.1021/jp209041x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use molecular docking and free energy calculations to estimate the relative free energy of binding of six arylamide compounds designed to inhibit the hDM2-p53 interaction. We show that using docking methods to predict or rank the binding affinity of a series of arylamide inhibitors of the hDM2-p53 interaction is problematic. However, using free energy calculations, we show that we can achieve levels of accuracy that can guide the development of novel arylamide compounds. We perform alchemical free energy calculations using the Desmond molecular dynamics package with the same arylamide inhibitors of the hDM2-p53 system and illustrate the challenges of performing accurate free energy calculations for realistic systems. To our knowledge, these are the first calculations for inhibitors of the hDM2 system that employ a full treatment of statistical mechanics including explicit water representation and full protein flexibility. We show that mutating three functional groups in a single transformation can be more efficient than mutating the groups one by one if proper intermediates are used. We also show that Hamiltonian exchanges can improve the efficiency of the calculation compared to standard alchemical methods, with a novel use of the phase space overlap to monitor sampling extent. We show that, despite sampling limitations, this approach can achieve levels of accuracy sufficient to bias further inhibitor modification toward binding, and identifies antiparallel configurations as stable or more stable than the parallel configurations that are typically considered.
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Affiliation(s)
- Jonathan C Fuller
- Institute of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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24
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Kim I, Allen TW. Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space. J Chem Phys 2012; 136:164103. [PMID: 22559466 DOI: 10.1063/1.3701766] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Free energy perturbation, a method for computing the free energy difference between two states, is often combined with non-Boltzmann biased sampling techniques in order to accelerate the convergence of free energy calculations. Here we present a new extension of the Bennett acceptance ratio (BAR) method by combining it with umbrella sampling (US) along a reaction coordinate in configurational space. In this approach, which we call Bennett acceptance ratio with umbrella sampling (BAR-US), the conditional histogram of energy difference (a mapping of the 3N-dimensional configurational space via a reaction coordinate onto 1D energy difference space) is weighted for marginalization with the associated population density along a reaction coordinate computed by US. This procedure produces marginal histograms of energy difference, from forward and backward simulations, with higher overlap in energy difference space, rendering free energy difference estimations using BAR statistically more reliable. In addition to BAR-US, two histogram analysis methods, termed Bennett overlapping histograms with US (BOH-US) and Bennett-Hummer (linear) least square with US (BHLS-US), are employed as consistency and convergence checks for free energy difference estimation by BAR-US. The proposed methods (BAR-US, BOH-US, and BHLS-US) are applied to a 1-dimensional asymmetric model potential, as has been used previously to test free energy calculations from non-equilibrium processes. We then consider the more stringent test of a 1-dimensional strongly (but linearly) shifted harmonic oscillator, which exhibits no overlap between two states when sampled using unbiased Brownian dynamics. We find that the efficiency of the proposed methods is enhanced over the original Bennett's methods (BAR, BOH, and BHLS) through fast uniform sampling of energy difference space via US in configurational space. We apply the proposed methods to the calculation of the electrostatic contribution to the absolute solvation free energy (excess chemical potential) of water. We then address the controversial issue of ion selectivity in the K(+) ion channel, KcsA. We have calculated the relative binding affinity of K(+) over Na(+) within a binding site of the KcsA channel for which different, though adjacent, K(+) and Na(+) configurations exist, ideally suited to these US-enhanced methods. Our studies demonstrate that the significant improvements in free energy calculations obtained using the proposed methods can have serious consequences for elucidating biological mechanisms and for the interpretation of experimental data.
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Affiliation(s)
- Ilsoo Kim
- Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616, USA.
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25
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Dirks RM, Xu H, Shaw DE. Improving Sampling by Exchanging Hamiltonians with Efficiently Configured Nonequilibrium Simulations. J Chem Theory Comput 2011; 8:162-71. [DOI: 10.1021/ct200464v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert M. Dirks
- D. E. Shaw Research, 120 W. 45th St., 39th Floor, New York, New York 10036, United States
| | - Huafeng Xu
- D. E. Shaw Research, 120 W. 45th St., 39th Floor, New York, New York 10036, United States
| | - David E. Shaw
- D. E. Shaw Research, 120 W. 45th St., 39th Floor, New York, New York 10036, United States
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, United States
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26
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Chodera JD, Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing. J Chem Phys 2011; 135:194110. [DOI: 10.1063/1.3660669] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Kim J, Straub JE. Generalized simulated tempering for exploring strong phase transitions. J Chem Phys 2011; 133:154101. [PMID: 20969364 DOI: 10.1063/1.3503503] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An extension of the simulation tempering algorithm is proposed. It is shown to be particularly suited to the exploration of first-order phase transition systems characterized by the backbending or S-loop in the statistical temperature or a microcanonical caloric curve. A guided Markov process in an auxiliary parameter space systematically combines a set of parametrized Tsallis-weight ensemble simulations, which are targeted to transform unstable or metastable energy states of canonical ensembles into stable ones and smoothly join ordered and disordered phases across phase transition regions via a succession of unimodal energy distributions. The inverse mapping between the sampling weight and the effective temperature enables an optimal selection of relevant Tsallis-weight parameters. A semianalytic expression for the biasing weight in parameter space is adaptively updated "on the fly" during the simulation to achieve rapid convergence. Accelerated tunneling transitions with a comprehensive sampling for phase-coexistent states are explicitly demonstrated in systems subject to strong hysteresis including Potts and Ising spin models and a 147 atom Lennard-Jones cluster.
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Affiliation(s)
- Jaegil Kim
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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28
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Abstract
Serial tempering is a computational method that turns the temperature T (or more generally any independent λ parameter) into a dynamical variable. It is shown that, under conditions for which this variable is fast, serial tempering is equivalent to the umbrella sampling method with a single effective potential. This equivalence is demonstrated using both a small one-dimensional system and a small solvated peptide. The suggestion is then made to replace the serial tempering protocol with the equivalent umbrella sampling calculation. This approach, serial tempering without exchange (STeWiE), has the same performance as serial tempering in the limit that exchanges are frequent, is simpler to implement, and has fewer adjustable parameters than conventional serial tempering. The equivalence of serial tempering and STeWiE also provides a convenient route for estimating and optimizing the performance of serial tempering simulations and other generalized-ensemble methods.
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Affiliation(s)
- Hugh Nymeyer
- The Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, USA.
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