I tried to run a 500ns MD simulation of a protein in Gromacs. Due to power failure, my pc turned of after around 450+ ns. Now I want to restart the simulation from that point. I used the following command-"gmx mdrun -v -deffnm md_0_1 -cpi md_0_1.cpt -append", but found that I dont have any cpt file. Now how should I do this? Is there any other way? If not, then how to generate the cpt file of my simulation?
Hi Nadim!
Are you sure that you have no cpt-file at all? It is very important for analysis (some tools in gromacs require cpt). If you have a cpt file which is named as state.cpt, then you can restart the simulation with the flag -noappend, instead of -append. After -cpi you shall write state.cpt and then either you write the new number of steps after -nsteps or just continue until it will finish.
Another option, which works strangely in gromacs sometimes (it can restart from the wrong time, like double time, but can start correctly as well) is to use mdp, trr and edr files. Then you will have to give in your mdp file the starting step and starting time (the time when you simulation crushed) and then process it with grompp, but name the tpr file differently, it can happen that the older trajectory might not be processed without the first tpr file. Then you run your simulation with the flag -s new.tpr. I would suggest you to observe the time in the new log-file in order to know if the restart happened correctly, from the right time. Otherwise, you might need again to return to mdp file and try to adjust start-time or start-step.
If your simulation had the name 'md_0_1' did you search for ' md_0_1_prev.cpt'? Maybe GROMACS failed in saving the final .cpt file but you should have the previous one that you can use to continue your simulation.
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