Hi Noureen!
This could also happen if you haven’t done any combination of the cpout files. A common cause for that is the cpout file or a replica or more were not included in the inputs. For N pH values, cphstats expects N inputs, individually derived from each replica.
From: Abdelrahman, Noureen <noureen.unc.edu>
Date: Tuesday, May 21, 2024 at 2:19 AM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: Merge cpout files to analyze full simulation
I merged the cpout files and made sure all replicas have the same length in the first simulation and same length in the restart, then created the reordered files using the following command: cphstats --fix-remd reordered_cpouts *cpout The reordered
I merged the cpout files and made sure all replicas have the same length in the first simulation and same length in the restart, then created the reordered files using the following command:
cphstats --fix-remd reordered_cpouts *cpout
The reordered files were created, but I got this warning message, and I am not sure what it means or whether it will affect my results:
WARNING: not all data records were assigned to a specific cpout file
this can happen, for instance, if you did *not* provide all
of the replica cpout files to cphstats to process. Check
your results carefully!
Have you encountered that warning before?
Thank you,
Noureen
________________________________
From: He, Amy <he.1768.buckeyemail.osu.edu>
Sent: Monday, May 20, 2024 6:33 PM
To: Abdelrahman, Noureen <noureen.unc.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Merge cpout files to analyze full simulation
I’ve done similar things before. The timestamps shouldn’t matter as long as the total length is consistent amongst all replicas, but please let me know if you find any further issues with this!
Amy
From: Abdelrahman, Noureen <noureen.unc.edu>
Date: Monday, May 20, 2024 at 6:16 PM
To: He, Amy <he.1768.buckeyemail.osu.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: Merge cpout files to analyze full simulation
Thanks, I've done that. But is it okay that in my combined. cpout file I have the same Timestep twice? For instance my time steps go like this: 100, 200, 300,. . . . 1000000 (from the first file), then 100, 200,. . . 1100000 (from the second file).
Thanks, I've done that. But is it okay that in my combined.cpout file I have the same Timestep twice? For instance my time steps go like this: 100, 200, 300,....1000000 (from the first file), then 100, 200,...1100000 (from the second file).
Noureen
________________________________
From: He, Amy <he.1768.buckeyemail.osu.edu>
Sent: Monday, May 20, 2024 9:42 AM
To: Abdelrahman, Noureen <noureen.unc.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Merge cpout files to analyze full simulation
Hi Noureen,
You can concatenate the first and second cpout files for each replica. Doing this might work:
cat first_rep.001.cpout second_rep.001cpout > combined_rep.001.cpout
Before you process and reorder (cphstats --fix-remd) the REMD data. All combined cpout files need to have the same length (number of data points) if I remember correctly.
Hope this helps!
Bests,
Amy H
From: Abdelrahman, Noureen via AMBER <amber.ambermd.org>
Date: Monday, May 20, 2024 at 9:10 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Merge cpout files to analyze full simulation
Hello everyone,
I was running a pH-REMD simulation that timed out, and I restarted it using the updated coordinates and cpin files. Now, I have two sets of cpout files that I need to merge for each pH to start my analysis. However, it doesn't seem that cphstats has a merge option. What is the best way to merge my cpout files to analyze the full simulation?
Thank you,
Noureen
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Received on Tue May 21 2024 - 07:30:02 PDT
