On 6/8/15 9:19 AM, Zhang, Cheng wrote:
Dear Gromacs expert, I was trying to extend my simulations. Relevant files can be found at https://copy.com/c8dDMnC0df2gbig9 To prepare the "md_0_1.tpr" file, I set the following in the "md_50ns.mdp" so that it can run 50 ns in total. nsteps = 25000000 dt = 0.002 Then I submit the same job for 5 times with the following command: gerun mdrun_mpi -deffnm md_0_1.tpr -cpi md_0_1.cpt -maxh 30 -append (Each of the 5 jobs would be hold until the previous one had finished.) However, as I check the 5 xtc files (e.g. RMSD): #md_0_1.tpr.xtc.1# #md_0_1.tpr.xtc.2# #md_0_1.tpr.xtc.3# #md_0_1.tpr.xtc.4# md_0_1.tpr.xtc all of them start the simulation from 0 to 10000 ps with different fluctuations. As I understand, they all start from the beginning instead of extending the simulation based on its previous one. So can I ask if I have done something incorrect?
If you're not modifying the contents of the .tpr file to indicate that you want to extend the simulation, mdrun is just going to run the same simulation. It's doing what you have told it to do. You need to invoke gmx convert-tpr (previously called tpbconv). See the wiki:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4_and_Newer -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (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 [email protected].
