I started protein ligand MD simulation in gromacs for 10ns. However due to cluster shutdown I had to restart it again. Md.tpr file of md is formed but it do not include portion after restart; How can I get tpr after restart. As for analysis of md trajectory tpr file is required; In this case I get only .tpr file before restart. Also log file completed 5000000 steps but it gave average of 1456026 steps using 14562 frames. I am not getting why it is so? I am surprised that my first MD job stopped at 2790000 steps (md_prod.log file) but it took restart from (3543975 steps). need suggestions.
If you have a .cpt file, include the following flags in your mdrun,
-cpi .cpt -append
if all files are being appended, if no then
-noappend
In order to restart the dynamics, you must continue from the existing check point file.
Command:
gmx mdrun -s .tpr -cpi .cpt -noappend
Outcome: .gro, .log, .edr and .xtc files
Afterwards, you need to combine both trajectories.
Command:
gmx trjcat -f .xtc .xtc -o .xtc -cat
-cat is used to merge the files in proper order.
Regards
Anu
Please take a look at your input and output file. To run MD .tpr file is required. Production run does not give a tpr file. check your output files such as (xtc, trr and edr etc.). gmx check will do the job. The information regarding steps and frames will be displayed on screen. So you can better understand, where frames are missing during simulation.
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