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Peng X, Zhang Y, Li Y, Liu Q, Chu H, Zhang D, Li G. Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations. J Chem Theory Comput 2018; 14:1216-1227. [DOI: 10.1021/acs.jctc.7b01211] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiangda Peng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Chinese
Academy of Science, University of Chinese Academy Sciences, Beijing 100049, P. R. China
| | - Yuebin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - QingLong Liu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Dinglin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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Wan B, Xu S, Zhou X. Effectively explore metastable states of proteins by adaptive nonequilibrium driving simulations. Phys Rev E 2017; 95:033304. [PMID: 28415335 DOI: 10.1103/physreve.95.033304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 06/07/2023]
Abstract
Nonequilibrium drivings applied in molecular dynamics (MD) simulations can efficiently extend the visiting range of protein conformations, but might compel systems to go far away from equilibrium and thus mainly explore irrelevant conformations. Here we propose a general method, called adaptive nonequilibrium simulation (ANES), to automatically adjust the external driving on the fly, based on the feedback of the short-time average response of system. Thus, the ANES approximately keeps the local equilibrium but efficiently accelerates the global motion. We illustrate the capability of the ANES in highly efficiently exploring metastable conformations in the deca-alanine peptide and find that the 0.2-μs ANES approximately captures the important states and folding and unfolding pathways in the HP35 solution by comparing with the result of the recent 398-μs equilibrium MD simulation on Anton [S. Piana et al., Proc. Natl. Acad. Sci. USA 109, 17845 (2012)PNASA60027-842410.1073/pnas.1201811109].
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Affiliation(s)
- Biao Wan
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shun Xu
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Wan B, Yang C, Wang Y, Zhou X. Jarzynski matrix equality: Calculating the free-energy difference by nonequilibrium simulations with an arbitrary initial distribution. Phys Rev E 2016; 93:043312. [PMID: 27176433 DOI: 10.1103/physreve.93.043312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Indexed: 06/05/2023]
Abstract
The Jarzynski equality (JE) method, which relates the work of a nonequilibrium process to the free-energy difference between its initial and final states, provides an efficient way to calculate free energies of thermodynamic systems in simulations or experiments. However, more extensive applications of the JE are hindered by the requirement that the initial state must be in equilibrium. In this work we extend the JE method to be the Jarzynski matrix equality (JME) method, which relates the work of trajectories connecting metastable conformational regions to their local free energies, and thus we can estimate the free energy from the nonequilibrium trajectories starting from an almost arbitrary initial distribution. We then apply the JME to toy models, Lennard-Jones fluids, and polymer chain models, demonstrating its efficiency in free-energy calculations with satisfactory accuracy. The JME extends the applicability of the nonequilibrium methods to complex systems whose initial equilibrium states are difficult to reach.
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Affiliation(s)
- Biao Wan
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Yang
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanting Wang
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Yang C, Wan B, Xu S, Wang Y, Zhou X. Equilibrium sampling by reweighting nonequilibrium simulation trajectories. Phys Rev E 2016; 93:033309. [PMID: 27078486 DOI: 10.1103/physreve.93.033309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Indexed: 06/05/2023]
Abstract
Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.
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Affiliation(s)
- Cheng Yang
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Biao Wan
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shun Xu
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanting Wang
- State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100086, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Systematically constructing kinetic transition network in polypeptide from top to down: trajectory mapping. PLoS One 2015; 10:e0125932. [PMID: 25962177 PMCID: PMC4427365 DOI: 10.1371/journal.pone.0125932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/24/2015] [Indexed: 11/23/2022] Open
Abstract
Molecular dynamics (MD) simulation is an important tool for understanding bio-molecules in microscopic temporal/spatial scales. Besides the demand in improving simulation techniques to approach experimental scales, it becomes more and more crucial to develop robust methodology for precisely and objectively interpreting massive MD simulation data. In our previous work [J Phys Chem B 114, 10266 (2010)], the trajectory mapping (TM) method was presented to analyze simulation trajectories then to construct a kinetic transition network of metastable states. In this work, we further present a top-down implementation of TM to systematically detect complicate features of conformational space. We first look at longer MD trajectory pieces to get a coarse picture of transition network at larger time scale, and then we gradually cut the trajectory pieces in shorter for more details. A robust clustering algorithm is designed to more effectively identify the metastable states and transition events. We applied this TM method to detect the hierarchical structure in the conformational space of alanine-dodeca-peptide from microsecond to nanosecond time scales. The results show a downhill folding process of the peptide through multiple pathways. Even in this simple system, we found that single common-used order parameter is not sufficient either in distinguishing the metastable states or predicting the transition kinetics among these states.
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Gong L, Zhou X. Kinetic Transition Network Based on Trajectory Mapping. J Phys Chem B 2010; 114:10266-76. [DOI: 10.1021/jp100737g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Linchen Gong
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 790-784, Korea, Institute for Advanced Study, Tsinghua University, Beijing 100080, China, and Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Xin Zhou
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 790-784, Korea, Institute for Advanced Study, Tsinghua University, Beijing 100080, China, and Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
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