[gmx-users] About MD

Jussi Lehtola jussi.lehtola at helsinki.fi
Mon Sep 26 11:19:48 CEST 2011

On Mon, 26 Sep 2011 09:31:39 +0200
xiaojing gong <xnzgxj at gmail.com> wrote:
> Hi, many thanks for your answer.
> >> Any dynamical simulation has a lowest-energy structure... whether
> >> this
> means anything is another question.
> I am just wondering whether the structures you find with MD determined
> mainly by thermodynamics  (i.e. the lowest energy structures) or by
> kinetics (i.e. the structures
> with the lowest activation barriers)?

The energy is NOT minimized in thermodynamics. The relevant quantity
that is minimized is the free energy. In NVT-simulations it's the
Helmholtz free energy
	F = E - TS
where T is temperature and S the entropy. The minimum of F is obtained
in the struggle of minimum energy and maximal entropy. E is, however,
minimized when T=0.

In NpT you minimize the Gibbs free energy
	G = E + pV -TS
where p is pressure and V is volume. Here to minimize E you would set
Mr. Jussi Lehtola, M. Sc.         Doctoral Student
jussi.lehtola at helsinki.fi         Department of Physics
http://www.helsinki.fi/~jzlehtol  University of Helsinki
Office phone: +358 9 191 50 632   Finland
Jussi Lehtola, FM                 Tohtorikoulutettava
jussi.lehtola at helsinki.fi         Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632

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