GROMACS version: 2019.4
GROMACS modification: No
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Dear all,
I am running concatenate simulations of the same system to obtain a long run but split in different parts (different xtc files) for better analysis. For that, each new simulation runs from the last frame of the previous using the -cpi flag. Here an example:
gmx convert-tpr -s prevFile.tpr -nsteps numSteps -o outFile.tpr
gmx mdrun -v -s outFile.tpr -cpi prevFile.cpt -deffnm outFile -noappend
I use the “noappend” flag to get different files and not a large one.
At some point I change the time step by calling another mdp file with the new time step, but using as starting point the previous checkpoint. THis is the only way I found to change time step since “gmx convert-tpr” has no option to change it:
gmx grompp -f newDt.mdp -c prevFile.pdb -r prevFile.pdb -t prevFile.cpt -p topol.top -o outFile.tpr
gmx mdrun -v -cpi prevFile.cpt -deffnm outFile -c outFile.pdb -noappend
My problem is that at this step, although the first frame of the new file and the last of the previous one match, the times in the log file don’t since GROMACS consider the new time step to compute the times. For example if in the previous file the time step was “dt=0.001” and finished at frame 1000, it finished at time 1ps according to log file. But if the new one starts at frame 1000 but time step is dt=0.002, the new starting time is 2000.
Is there any option in GROMACS to avoid this issue? I know it is possible to modify the xtc files after simulation, but it would be nice if it could be done during run.
Thank you in andvance,
María