[gmx-users] system far from the equilibration state

Shima Arasteh shima_arasteh2001 at yahoo.com
Thu Feb 7 10:50:01 CET 2013

Thanks for your reply. 
How would I know that when I get close to the equilibration state?  By Pressure, Temperature,or  RMSD plots?

Thanks in advance for your suggestions.


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: Monday, February 4, 2013 11:37 PM
Subject: Re: [gmx-users] system far from the equilibration state

On 2/4/13 2:04 PM, Shima Arasteh wrote:
> Hi,
> I am simulating a system of peptide/membrane/water. If my system is far from the equilibration, would that be correct if I use Berendsen pressure coupling for nano seconds to do NPT equilibration and then change it to Parrinello-Rahman to get the true pressure? Anybody may suggest me please?

Sounds reasonable.  Berendsen is a useful method in such cases.



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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