[gmx-users] Re:problem with simulation of freezing of water

ran friedman ran.friedman at gmail.com
Sun Nov 11 20:27:44 CET 2012


Also note that it is difficult to simulate the right structure of ice (Ih).
You didn't write what you want to study, but search the literature
carefully. You may need to use an ab-initio model.


Message: 7
Date: Sun, 11 Nov 2012 11:26:19 -0500
From: Justin Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Re:problem with simulation of freezing of
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <509FD1AB.50400 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed

On 11/11/12 11:22 AM, Ali Alizadeh wrote:
> Dear Justin
> Thank you for reply,
> I want to simulation of water freezing, my condition:
> pressure=300 bar and T=240 k , number 1656, run time= 100ns,
> I can not see regular structure of ice by MD simulation or by gromacs?
> In your opinion, if i want this structure of ice for my simulation,
> What can i do?

Start by searching the literature for a suitable protocol.  Ice simulations
been done before.  As I said before, each water model has a different
point, and hardly any of them correspond to the actual experimental value.
if you can produce a suitable simulation with a pressure of 1 bar (proof of
concept) and then change conditions.

What you have to keep in mind is that most water models were designed to
work at
ambient conditions for "normal" simulations.  They do not necessarily work
extremes or produce useful results under those conditions.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080



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