[gmx-users] system far from the equilibration state

[Shima Arasteh]

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.

Sincerely,
Shima


________________________________
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

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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