[gmx-users] Restart MD with overwritten CPT using TRR file in gromacs/2016.3

[Abramyan, Tigran]

Thanks a lot for your response, Mark,


Your response did not come to my email, but I found it via Gromacs website. I think my email is registered on your site, but I forgot my Username. Is there a way to login with the email address and password? At the moment it looks like the only way I can reply to your response is via this email? Please suggest the correct way if I am wrong here.


So, as for the issue, it looks like Gromacs has two CPT files, both of which got rewritten when the job got resubmitted after crashing. The names of these CPT files are md.cpt and md_prev.cpt, and both have the same writing time (the current time, as the job is running now). I do not see any #md.cpt or #md_prev.cpt files, which I could use to restart the job from the time (frame and velocities) when it crashed.


I am thinking of ways to go around this issue and would like to (1) extract the last frame from the TRR file and (2) use the TRR file to read the velocities from. So, for the first step I do the following:


cp #md.trr.1# md.trr  (is this correct, by the way?)

echo "0" | gmx trjconv -f md.trr -s md.tpr -o lasframe.gro -b lastframe -e lastframe


But I still obtain the same error, which makes me suspect something is wrong with the #md.trr.1# file?


Program:     gmx trjconv, version 2016.3
Source file: src/gromacs/fileio/trrio.cpp (line 114)

Fatal error:
Failed to find GROMACS magic number in trr frame header, so this is not a trr
file!



--
Tigran M. Abramyan, Ph.D.
Postdoctoral Fellow, Computational Biophysics & Molecular Design
Center for Integrative Chemical Biology and Drug Discovery
Eshelman School of Pharmacy
The University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7363

________________________________
From: Abramyan, Tigran
Sent: Friday, October 27, 2017 4:24:15 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Restart MD with overwritten CPT using TRR file in gromacs/2016.3


Hi,


Because one of my gromacs/2016.3 jobs accidentally crashed and got restarted and overwrote the CPT file, I am now attempting to continue a simulation using the TRR file. For this I ran the command 'gmx convert-tpr -s md.tpr -f md.trr -o md_next.tpr', so that I could use 'md_next.tpr' file to restart the simulation, but obtain the following error:


READING COORDS, VELS AND BOX FROM TRAJECTORY md.trr...

trr version: GMX_trn_file (single precision)
Read    trr frame   7519: step 150380000 time  300760.000
-------------------------------------------------------
Program:     gmx convert-tpr, version 2016.3
Source file: src/gromacs/fileio/trrio.cpp (line 114)

Fatal error:
Failed to find GROMACS magic number in trr frame header, so this is not a trr
file!



The same command (only replace 'gmx convert' to older version 'tpbconv') works fine in gromacs/4.6.3.


Additionally, I was wondering, why doesn't gromacs automatically 'hash' backup the CPT file along with the other files? Does that mean that CPT file probably has info (e.g., velocities) from the previous run, which didn't get overwritten?


Please help.


--
Tigran M. Abramyan, Ph.D.
Postdoctoral Fellow, Computational Biophysics & Molecular Design
Center for Integrative Chemical Biology and Drug Discovery
Eshelman School of Pharmacy
The University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7363