Re: [AMBER] relaxation time CphMD

From: Jason Swails <>
Date: Fri, 13 Nov 2015 10:59:08 -0500

On Fri, Nov 13, 2015 at 10:03 AM, Arjun Sharma <>

> Dear Jason,
> I’m 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 ?

​You need to figure this out by carefully analyzing the cpout file. Blank
lines separate protonation state exchange attempts. So look at an exchange
attempt, which gives you a specific residue in a specific state. Look back
through the cpout file and see the last time that residue was specified.
If it was in a different state, an exchange occurred on that step.

I don’t 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 ?

I plotted this quantity in the paper (see figure
 in DOI


​. There are two ways you could generate that data. The first is how
Brian suggested (I *think* this is what I did, although it has been many
years since I ran that particular part of the calculation). The latter is
to modify the source code and have sander or pmemd print out energies for
the relaxation dynamics. I only did that calculation for ACFCA, which is a
tiny system where the titrating residues are highly solvent-exposed. So
this presents on average a worst-case scenario for how slowly the system
relaxes to the new charges.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 13 2015 - 08:00:06 PST
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