Re: [AMBER] Restarting pH-REMD simulations after abnormal termination

From: Cruzeiro,Vinicius Wilian D <>
Date: Fri, 13 Oct 2017 14:07:18 +0000

Hello Eric,

Correct, the cprestrt files are written according to the ntwr variable (same variable that controls how often the coordinate restart file will be written) or at the end of the simulation.

Cpout files start with the protonation state of each titratable residue at the initial step of the simulation. Then, it contains the protonation state after each protonation attempt. However, these information are not written to the cpout files instantaneously after a protonation attempt is made! On the same way that happens with the mdout files, the data to be printed is accumulated and is flushed to the output files less frequently.

Currently, cphstats cannot do "exactly" what you said. However, it has some nice analysis options (cumulative and chunk) that might work for what you need. As you are doing pH-REMD, I wouldn't try to manually edit the cpout files before reordering them.

I hope this helps.


Vinícius Wilian D Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633

From: Eric Lang <>
Sent: Thursday, October 12, 2017 9:55:28 AM
Subject: [AMBER] Restarting pH-REMD simulations after abnormal termination

Dear Amber users,

I was running a 100 ns pH-REMD simulation when the communication with one of the GPU node stopped and the simulation crashed before the end.

I would like to restart my simulation.

Based on the time stamp the cpin files seem to have been written at the same time as my restart file (which I set up to be written every 1 ns).

Is it a general behaviour for the cpin files to be written at the same frequency as the restart files? If so I guess I can safely restart my simulations from the last restarted files.

I believe the cpout files are written much more often, could you please let me know the frequency at which they are written? is it the number of protonation change attempts?

Is there a way in cphstats to select the number of steps we want to use in a cpout file for analysis? Or if I want to do it should I manually edit my cpout files?

Many thanks in advance for your help,


Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Fri Oct 13 2017 - 07:30:02 PDT
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