发信人: overdrive (超载), 信区: Biology
标 题: Re: 哪位了解Amber？
发信站: The unknown SPACE (Fri Sep 27 15:24:15 2002), 转信


Force field is a classical treatment of the
molecular system, also called molecular mechanics (MM)
(compared to Quantum mechanics - QM). It seperate
the molecular energy as several parts, say,
bond stretch, angle, torsions, VDW, electronstatic
interaction ... Each type of energy can be assign
a function form (mostly a harmonic osillator),
for example, for bond strech interal energy:
E(r) = k(r-re)^2,
while r is the actual bond distance in the molecular
geometry, re is equilibrium bond distance, and k is the
force constant.

The k and re in this case are empirical parameters,
and the basic assumpiton for MM is those parameters are
transferable from system to system. One can obtain force
field parameters from either experimental results (mostly
for non-bonding parameters, say, VDW term) or electronic
structure calculations (mostly for bonding properties) or
a combo of those. Different packages, AMBER, CHARMM, or
whatever may use different set of parametrization, but the basic
idea is the same: decide description the functional form
->parametrization -> obtain transferable parameters.








【 在 blaudonau (Alps) 的大作中提到: 】
: 力场都是对小分子进行模拟得到的
: 通常是比较密度,heat of vaporization,hydration free energy etc
: 然后将他们延伸到生物分子体系
: 比较"amazing"的是参数话的时候只考虑了
: 热力学的性质
: 但是力场基本上都能比较正确的描述
: 动力学性质
: 象order parameter之类的从nmr得到的参数
: MD能reproduce
: 【 在 centerwise (centerwise) 的大作中提到: 】
: : 一种计算分子作用的Force Field，
: : 但是不知道计算使用的参数怎么得到？哪位了解的能不能说一下


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