Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data

被引:80
作者
White, Andrew D.
Voth, Gregory A. [1 ]
机构
[1] Univ Chicago, James Franck Inst, Dept Chem, Inst Biophys Dynam, Chicago, IL 60637 USA
关键词
BATTERY ELECTROLYTES; ETHYLENE CARBONATE; FORCE-FIELDS; DYNAMICS; REFINEMENT; MODEL; POTENTIALS; ALGORITHMS; CHEMISTRY;
D O I
10.1021/ct500320c
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
A primary goal in molecular simulations is to modify the potential energy of a system so that properties of the simulation match experimental data. This is traditionally done through iterative cycles of simulation and reparameterization. An alternative approach is to bias the potential energy so that the system matches experimental data. This can be done while minimally changing the underlying free energy of the molecular simulation. Current minimal biasing methods require replicas, which can lead to unphysical dynamics and introduces new complexity: the choice of replica number and their properties. Here, we describe a new method, called experiment directed simulation that does not require replicas, converges rapidly, can match many data simultaneously, and minimally modifies the potential. The experiment directed simulation method is demonstrated on model systems and a three-component electrolyte simulation. The theory used to derive the method also provides insight into how changing a molecular force-field impacts the expected value of observables in simulation.
引用
收藏
页码:3023 / 3030
页数:8
相关论文
共 43 条
[1]   A general purpose model for the condensed phases of water: TIP4P/2005 [J].
Abascal, JLF ;
Vega, C .
JOURNAL OF CHEMICAL PHYSICS, 2005, 123 (23)
[2]  
[Anonymous], 2010, COLT 10 P 23 ANN C L
[3]   Reactions of Singly-Reduced Ethylene Carbonate in Lithium Battery Electrolytes: A Molecular Dynamics Simulation Study Using the ReaxFF [J].
Bedrov, Dmitry ;
Smith, Grant D. ;
van Duin, Adri C. T. .
JOURNAL OF PHYSICAL CHEMISTRY A, 2012, 116 (11) :2978-2985
[4]   An integral equation to describe the solvation of polar molecules in liquid water [J].
Beglov, D ;
Roux, B .
JOURNAL OF PHYSICAL CHEMISTRY B, 1997, 101 (39) :7821-7826
[5]   Determination of protein structures consistent with NMR order parameters [J].
Best, RB ;
Vendruscolo, M .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2004, 126 (26) :8090-8091
[6]   How to derive and parameterize effective potentials in colloid-polymer mixtures [J].
Bolhuis, PG ;
Louis, AA .
MACROMOLECULES, 2002, 35 (05) :1860-1869
[7]   Combining Experiments and Simulations Using the Maximum Entropy Principle [J].
Boomsma, Wouter ;
Ferkinghoff-Borg, Jesper ;
Lindorff-Larsen, Kresten .
PLOS COMPUTATIONAL BIOLOGY, 2014, 10 (02)
[8]   Quantum Chemistry and Molecular Dynamics Simulation Study of Dimethyl Carbonate: Ethylene Carbonate Electrolytes Doped with LiPF6 [J].
Borodin, Oleg ;
Smith, Grant D. .
JOURNAL OF PHYSICAL CHEMISTRY B, 2009, 113 (06) :1763-1776
[9]   COMPUTATIONAL CHALLENGES FOR MACROMOLECULAR STRUCTURE DETERMINATION BY X-RAY CRYSTALLOGRAPHY AND SOLUTION NMR-SPECTROSCOPY [J].
BRUNGER, AT ;
NILGES, M .
QUARTERLY REVIEWS OF BIOPHYSICS, 1993, 26 (01) :49-125
[10]   Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle [J].
Cavalli, Andrea ;
Camilloni, Carlo ;
Vendruscolo, Michele .
JOURNAL OF CHEMICAL PHYSICS, 2013, 138 (09)