Hi all, I tried to run this gromacs tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html) in order to understand how checkpoint/restart works in Gromacs-5.1.2.
Based on running that tutorial I found that mdrun automatically checkpoint even though I didn't specify -cpt option (based on mdrun manual page, by default checkpoint every 15 minutes) 1. What if I specify -cpt option with a value longer than or smaller than 15 minutes ? does -cpt value will automatically override the default ? 2. I run the following command to restart production MD step (using SLURM) from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from previous mdrun execution. is my command right ? I just want to make sure. #!/bin/bash #SBATCH -J Lysozyme #SBATCH -o md-%j.out #SBATCH -A necis #SBATCH -N 3 #SBATCH -n 24 #SBATCH --time=144:00:00 #SBATCH --mail-user=hus...@gmail.com #SBATCH --mail-type=begin #SBATCH --mail-type=end mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1 Thank you in advance Regards, Husen On Sun, Apr 24, 2016 at 7:57 PM, Husen R <hus...@gmail.com> wrote: > Hi, > > Thanks a lot ! > I'll try it,.. > > Regards, > > > Husen > > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 4/24/16 12:04 AM, Husen R wrote: >> >>> Dear all, >>> >>> is there any complete documentation discussing checkpoint/restart in >>> Gromacs-5.1.2 ? >>> I found this link that discuss checkpoint ( >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and >>> this link that discuss restart ( >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these >>> are >>> not specifically for gromacs 5.1.2. >>> >>> >> There are no differences for 5.1.2, so that information is all relevant. >> >> -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 >> >> 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. >> > > -- 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.