Molecular Dynamics Using Nonvariational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation, and Application to the Bond Capacity Model

被引:13
作者
Poier, Pier Paolo [1 ]
Lagardere, Louis [2 ,3 ]
Piquemal, Jean-Philip [4 ,5 ,6 ]
Jensen, Frank [1 ]
机构
[1] Aarhus Univ, Dept Chem, Langelandsgade 140, DK-8000 Aarhus, Denmark
[2] Sorbonne Univ, Inst Parisien Chim Phys & Theor, F-75005 Paris, France
[3] Sorbonne Univ, Inst Sci Calcul & Donnees, F-75005 Paris, France
[4] Sorbonne Univ, Lab Chim Theor, F-75005 Paris, France
[5] Sorbonne Univ, Inst Univ France, F-75005 Paris, France
[6] Univ Texas Austin, Dept Biomed Engn, Austin, TX 78712 USA
基金
欧洲研究理事会;
关键词
POTENTIAL FUNCTIONS; SCALABLE EVALUATION; FLUCTUATING CHARGE; ENERGY DERIVATIVES; SIMULATIONS; EQUALIZATION; PARAMETERS; PROTEINS; SYSTEMS; SPACE;
D O I
10.1021/acs.jctc.9b00721
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
We extend the framework for polarizable force fields to include the case where the electrostatic multipoles are not determined by a variational minimization of the electrostatic energy. Such models formally require that the polarization response is calculated for all possible geometrical perturbations in order to obtain the energy gradient required for performing molecular dynamics simulations. By making use of a Lagrange formalism, however, this computationally demanding task can be replaced by solving a single equation similar to that for determining the electrostatic variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for nonvariational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields.
引用
收藏
页码:6213 / 6224
页数:12
相关论文
共 65 条
[1]   ATOM DIPOLE INTERACTION MODEL FOR MOLECULAR POLARIZABILITY - APPLICATION TO POLYATOMIC-MOLECULES AND DETERMINATION OF ATOM POLARIZABILITIES [J].
APPLEQUIST, J ;
CARL, JR ;
FUNG, KK .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1972, 94 (09) :2952-+
[2]   The midpoint method for parallelization of particle simulations [J].
Bowers, Kevin J. ;
Dror, Ron O. ;
Shaw, David E. .
JOURNAL OF CHEMICAL PHYSICS, 2006, 124 (18)
[3]   CHARMM: The Biomolecular Simulation Program [J].
Brooks, B. R. ;
Brooks, C. L., III ;
Mackerell, A. D., Jr. ;
Nilsson, L. ;
Petrella, R. J. ;
Roux, B. ;
Won, Y. ;
Archontis, G. ;
Bartels, C. ;
Boresch, S. ;
Caflisch, A. ;
Caves, L. ;
Cui, Q. ;
Dinner, A. R. ;
Feig, M. ;
Fischer, S. ;
Gao, J. ;
Hodoscek, M. ;
Im, W. ;
Kuczera, K. ;
Lazaridis, T. ;
Ma, J. ;
Ovchinnikov, V. ;
Paci, E. ;
Pastor, R. W. ;
Post, C. B. ;
Pu, J. Z. ;
Schaefer, M. ;
Tidor, B. ;
Venable, R. M. ;
Woodcock, H. L. ;
Wu, X. ;
Yang, W. ;
York, D. M. ;
Karplus, M. .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (10) :1545-1614
[4]   The Amber biomolecular simulation programs [J].
Case, DA ;
Cheatham, TE ;
Darden, T ;
Gohlke, H ;
Luo, R ;
Merz, KM ;
Onufriev, A ;
Simmerling, C ;
Wang, B ;
Woods, RJ .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) :1668-1688
[5]   MOLECULAR-DYNAMICS SIMULATIONS ON SOLVATED BIOMOLECULAR SYSTEMS - THE PARTICLE MESH EWALD METHOD LEADS TO STABLE TRAJECTORIES OF DNA, RNA, AND PROTEINS [J].
CHEATHAM, TE ;
MILLER, JL ;
FOX, T ;
DARDEN, TA ;
KOLLMAN, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (14) :4193-4194
[6]   Electrical response in chemical potential equalization schemes [J].
Chelli, R ;
Procacci, P ;
Righini, R ;
Califano, S .
JOURNAL OF CHEMICAL PHYSICS, 1999, 111 (18) :8569-8575
[7]   QTPIE:: Charge transfer with polarization current equalization.: A fluctuating charge model with correct asymptotics [J].
Chen, Jiahao ;
Martinez, Todd J. .
CHEMICAL PHYSICS LETTERS, 2007, 438 (4-6) :315-320
[8]   Correlation between electronic and molecular structure distortions and vibrational properties. I. Adiabatic approximations [J].
Cho, MH .
JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (08) :3480-3490
[9]   Model potential study of non-valence correlation-bound anions of (C60)n clusters: the role of electric field-induced charge transfer [J].
Choi, Tae Hoon ;
Jordan, Kenneth D. .
FARADAY DISCUSSIONS, 2019, 217 :547-560
[10]   A hybrid neutron diffraction and computer simulation study on the solvation of N-methylformamide in dimethylsulfoxide [J].
Cordeiro, Joao M. M. ;
Soper, Alan K. .
JOURNAL OF CHEMICAL PHYSICS, 2013, 138 (04)