[gmx-users] system far from the equilibration state

[Justin Lemkul]

On 2/7/13 4:50 AM, Shima Arasteh wrote:
>
> Thanks for your reply.
> How would I know that when I get close to the equilibration state?  By Pressure, Temperature,or  RMSD plots?
>

There are no absolutes, and it also depends on what one means by "converged" or 
"equilibrated."  If we're talking about initial NVT/NPT equilibration steps 
where the solute of interest is restrained in some way, simple analysis of 
temperature and pressure is likely sufficient to demonstrate that the ensemble 
is stable.  If we're talking about trying to determine equilibrium sampling, 
that's something else entirely and likely will involve protein-specific and/or 
lipid-specific metrics.

-Justin

>
> 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
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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