[gmx-users] Interuption Simulation

Negar Parvizi negar.parvizi at yahoo.com
Sat Aug 30 13:20:53 CEST 2014

Dear Gromacs users
I have submitted a simulation for 10 ns. Now when I started to plot the graphs such as RMSD, I saw that it has stopped at 8 ns. The point is that although the run has stopped before specified time, I see in md.log file the time report for the simulation, the same as report that I get for completed runs. I wanted to know the reason for that? (I should also mention that when I check the upper part of the md.log file, I see that the run has stopped at about 8 ns)

** The other thing is about continuing the simulation. For example I want to continue that run for the more 2 ns. I am using gromacs 4.5.4
I followed the instruction in gromacs website about extending simulations and used these two commands

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt
now my question is that when I choose timetoextendedby equal to 2000 ps and the simulation finishes,  where will be written the information of that 2 ns, I mean the .gro, .edr and other informations. Should I specify the deffname similar to that I used before for that 8 ns.

I am not sure whether the gromacs will overwrite the previous files or will edit them and add the information of that 2 ns at the end of previous .gro and .edr and . trj files.

Your prompt response would be greatly appreciated.

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