On 8/20/14, 6:33 AM, Dawid das wrote:
Dear Gromacs experts, I googled for answer and I found these: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_10000_ps but still I am confused about what happens in my simulation. I did 5 ns simulation and I would like to add extra 5 ns on top of that so that new results (energies, temperature, trajectory, etc.) will be appended to already existing files after first 5 ns simulation. Now I used this command to run MD simulation for the first time: \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e mCherry7-npt-md.edr > $CURDIR/mCherry7-npt-md.log 2>&1 After this in the same directory I run: tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr \$MDRUN -s npt-md-ext.tpr -cpi state.cpt I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same that means temperature, energies, etc. are the same as if I started from 0ns step, not from 5ns step of previous simulation. What can cause that? Is it because of used files names or I did something else wrong?
What does the .log file say? It should clearly indicate if the restart was done by reading in the checkpoint file.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
