Re: [AMBER] relaxation time CphMD

From: Brian Radak <brian.radak.accts.gmail.com>
Date: Fri, 13 Nov 2015 09:41:20 -0600

Isn't the relaxation MD discarded outright? That is, the MC step has the
appearance of also generating a new configuration corresponding to the
last step of the MD. All of the steps within that procedure are presumed
to have effectively incorrect Boltzmann weights and therefore are
"uninteresting."

Presumably you could do this "by hand" using a bunch of random
configurations and ParmEd. That is, run a simulation with fixed
protonation state, generate a new prmtop after changing the protonation
state and then run short MD with the new prmtop.

HTH,
Brian

On 11/13/2015 09:03 AM, Arjun Sharma wrote:
> Dear Jason,
>
> Iím trying to optimize the relaxation time in explicit solvent CpHMD. Is there anyway I can know at what production run (step #) the monte carlo exchange takes place ? I donít see that information in cpout file. I want to see how long it takes for the system to completely relax after each monte carlo step ( potential energy degradation overtime plot would be useful). Could you suggest a way to check this ?
>
> Thanks.
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-- 
Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
email: radak.uchicago.edu
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Received on Fri Nov 13 2015 - 08:00:03 PST
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