[gmx-users] NPT and NVT eqquilibruim - membrane simulation

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Oct 6 12:10:45 CEST 2012

 Thank you Justin.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, October 6, 2012 1:26 PM
Subject: Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation

On 10/6/12 3:15 AM, Shima Arasteh wrote:
>   In my own, I want to simulate POPC-water and then insert a protein in it. Then run a new simulation for my new system.
> I got the starting structure from Prof.Klauda website. Then dear Peter provides this link to get some useful files: http://uab.hyperfine.info/~pcl/files/popc36/
> Regarding to the pblished paper, written by Peter, NPT equilibration had been done. I also followed them and did the NPT. But now, I'm wondering when NPT is needed to be done and when NPT & NVT are both needed?

As long as the system is stable and you obtain converged observables, then there's nothing wrong with doing NPT as your only equilibration.  Not all systems are very well behaved and do require NVT first before switching on pressure coupling, so it is often advisable.  There are no hard and fast rules for equilibration, however.  Every system is different, so a universal recipe is not really possible.  If your method worked, then you're fine.


-- ========================================

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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