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. Thanks Regards N.Parvizi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
