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 <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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
--
========================================
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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