Multiple steering molecular dynamics applied to water exchange at alkali ions

被引:15
作者
Cascella, M
Guidoni, L
Maritan, A
Rothlisberger, U
Carloni, P
机构
[1] SISSA, ISAS, I-34014 Trieste, Italy
[2] Abdus Salaam Int Ctr Theoret Phys, I-34014 Trieste, Italy
[3] Swiss Fed Inst Technol, Dept Chem, CH-8093 Zurich, Switzerland
关键词
D O I
10.1021/jp026209b
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
The novel fast-growth or multiple steering molecular dynamics (MSMD) technique has been recently developed by Jarzynski to calculate free energy profiles along general transformation pathways (Phys. Rev. Lett. 1997, 78, 2690-2693; Phys. Rev. E 1997, 56,5018-5035).(1,2) Here, we apply this approach to calculate free energy barriers involved in the water exchange reaction of Na+ and K+ in aqueous solution. We investigate the influence of the key parameters of the MSMD simulations-the steering velocity, the sampling of the initial configurations, and the force constant-on the free energy. furthermore, we use this approach to describe energetical and structural features of the water exchange reaction of Na+ and K+ in aqueous solution. The MSMD technique turns out to be an efficient and fast convergent tool to enhance the sampling of rare chemical events with-the help of nonequilibrium forces.
引用
收藏
页码:13027 / 13032
页数:6
相关论文
共 41 条
[1]  
AQVIST J, 1990, J PHYS CHEM-US, V94, P8021, DOI 10.1021/j100384a009
[2]   Reconstructing potential energy functions from simulated force-induced unbinding processes [J].
Balsera, M ;
Stepaniants, S ;
Izrailev, S ;
Oono, Y ;
Schulten, K .
BIOPHYSICAL JOURNAL, 1997, 73 (03) :1281-1287
[3]   MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].
BERENDSEN, HJC ;
POSTMA, JPM ;
VANGUNSTEREN, WF ;
DINOLA, A ;
HAAK, JR .
JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690
[4]   The role and perspective of a initio molecular dynamics in the study of biological systems [J].
Carloni, P ;
Rothlisberger, U ;
Parrinello, M .
ACCOUNTS OF CHEMICAL RESEARCH, 2002, 35 (06) :455-464
[5]  
CASE DA, 1997, AMBER VERSION 5
[6]   Path-ensemble averages in systems driven far from equilibrium [J].
Crooks, GE .
PHYSICAL REVIEW E, 2000, 61 (03) :2361-2366
[7]   PARTICLE MESH EWALD - AN N.LOG(N) METHOD FOR EWALD SUMS IN LARGE SYSTEMS [J].
DARDEN, T ;
YORK, D ;
PEDERSEN, L .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (12) :10089-10092
[8]   A SMOOTH PARTICLE MESH EWALD METHOD [J].
ESSMANN, U ;
PERERA, L ;
BERKOWITZ, ML ;
DARDEN, T ;
LEE, H ;
PEDERSEN, LG .
JOURNAL OF CHEMICAL PHYSICS, 1995, 103 (19) :8577-8593
[9]   ADHESION FORCES BETWEEN INDIVIDUAL LIGAND-RECEPTOR PAIRS [J].
FLORIN, EL ;
MOY, VT ;
GAUB, HE .
SCIENCE, 1994, 264 (5157) :415-417
[10]   Ligand binding: Molecular mechanics calculation of the streptavidin biotin rupture force [J].
Grubmuller, H ;
Heymann, B ;
Tavan, P .
SCIENCE, 1996, 271 (5251) :997-999