21 okt 2012 kl. 09.22 skrev Shima Arasteh: > Hi again, > > I have done mdrun for 5000000 steps (10 ns) and got the results. Then I tried > to extend the simulation for another 5000000 steps ( I mean the next 10 ns = > 10 to 20 ns ) using this command: > # tpbconv -s md.tpr -o md.tpr -extend 10000 > # mpirun -np 32 mdrun_mpi -s md.tpr -o md.trr -c md.gro -e md.edr -g md.log > -cpi md.cpt -v > > The simulation started from step 5000000. I got the results as I expected : > whole 20ns simulation. > > Then I tried to extend the simulation for another 10ns ( I mean 20ns to 30ns > ). So used the last commands again, but the simulation starts from the step > 500000. However, I expect it to start from the step 10000000!
It looks like you're mixing up your cpt files. Since you didn't specify a filename for -cpo I bet your simulation produced "state.cpt", so you need to instruct mdrun to use that one as cpt input. > > Isn't it possible to extend a simulation for the second, third,... time? > > > What's the problem? Would you please help me? > > > Sincerely, > Shima > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
