[gmx-users] Reg; MD of DCE part II

Mark Abraham mark.abraham at anu.edu.au
Mon Oct 25 10:03:58 CEST 2010

----- Original Message -----
From: vinothkumar mohanakrishnan <kmvinoth at gmail.com>
Date: Monday, October 25, 2010 18:10
Subject: Re: [gmx-users] Reg; MD of DCE part II
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi mark >   > The system was well equiulibrated and the average temperature is 299.18 K and the pressure is 1.25 bar.

... and this means the system wants to contract (if this is an average pressure you've measured over a meaningful length of time).

> I checked in the manual (gromacs version 4.0)l and there is no section like 3.4.9 and i as well checked 7.3.15.

OK, well look up in those chapters what GROMACS will do with pressure coupling (and plan to upgrade GROMACS).

> i too know that when there is no pressure coupling the box size wont change. what one will do if one wants to do in the NPT ensemble and wants to control the box dimensions?

Given dimensions for a system at a given temperature are only compatible with a certain equilibrium pressure. PV=nRT and all that. You have to equilibrate to your reference pressure before you can expect the volume to stay within a small fluctuation of an average, and cannot choose P, V and T arbitrarily.


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