Hi Alessandra,
I followed the tutorial page you sent. Checkpoint files (.cpt) are binary files. So, there doesn’t seem to be a question of manual edit. In that case, it appeared that just adding -cpi latest .cpt to the ‘mdrun’ command would serve the purpose of the desired extension. However, there was some renaming done to the output files and hence mismatches were found with respect to information obtained from the latest .cpt file when I ran mdrun with the -cpi option. I tried editing the latest (binary) .cpi file from a vi editor to match the new names (.log, .edr, .trr, .xtc) using the :1,$s/old/new substituion, it resulted in the desired changes in the file but in the process, the file was said to be corrupted. I shall avoid doing this in the future.
Then I found in the tutorial page it says:
A simulation can be continued by reading the full state from file with option -cpi . This option is intelligent in the way that if no checkpoint file is found, GROMACS just assumes a normal run and starts from the first step of the [.tpr](http://manual.gromacs.org/current/reference-manual/file-formats.html#tpr) file.
So, I opted to add (to the mdrun command) the option -cpi without specifying any (.cpt) filename.
nohup gmx mdrun -pin on -pinoffset 0 -reprod -v -deffnm 6vw1_AE-orig_md_30ns -cpi &
It is running at the moment (5 ns in a 24-core server, said to be taking ~16 hrs). I assume that it will produce only but an extension from where I ended last and that latest the .tpr is read (according to the above-quoted part of the tutorial), though, I am not sure whether information related to the latest velocities were recorded in the latest .tpr (from where originally the discussion started).
In the nohup.out I found that the desired .tpr was indeed read.
Back Off! I just backed up 6vw1_AE-orig_md_30ns.log to ./#6vw1_AE-orig_md_30ns.log.1# Reading file 6vw1_AE-orig_md_30ns.tpr, VERSION 2020.3 (single precision) Changing nstlist from 10 to 100, rlist from 1.2 to 1.343
Could you possibly suggest if it should produce an extension only (in this way)?
Thanks again and kind regards,
Sankar