Dear Justin, Suppose at the end of NVT equilibation and before the start of the following NPT equilibation, I intentionally (or by accident) delete the nvt_prev.cpt file from the directory, does it affect the run of the NPT equilibation step?
Brett At 2016-04-05 21:27:41, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/5/16 9:24 AM, Brett wrote: >> Dear All, >> >> Based on the on-line Lysozyme tutorial, I started a MD from energy >> minimization to NVT equlibation to NPT equlibration, and I am now in the >> production MD step. >> >> When I checked my Directory containing all the MD files for the whole MD >> process, I find there is a "mdout.mdp". Is my understanding correct on that, >> in the energy minimization step, it will create a "mdout.mdp" file, and in >> any of the following of NVT equlibation, NPT equlibration and production MD >> step, a "mdout.mdp" file will be created and automatically replaced the >> "mdout.mdp" file created in the previous step? >> > >GROMACS backs up files, it doesn't replace them unless you set >GMX_MAXBACKUP=-1. > >> As I mentioned, currently I was in the production M step, and if I >> intentionally delete the "mdout.mdp" file from the Directory, how does it >> affect my production MD? >> > >mdout.mdp is just to record your options for posterity. Deleting it has no >effect on anything. > >> The next question, during my production MD step, I checked my Directory, and >> here let me take the NVT related files as example, I found there were a >> nvt.cpt and a nvt_prev.cpt file. Suppose my NVT equilibration step lasts for >> 100 ps, is the nvt.cpt the file created by "gmx grompp -f npt.mdp -c nvt.gro >> -t nvt.cpt -p topol.top -o npt.tpr", and the nvt_prev.cpt the cpt file >> created at the end of "gmx mdrun -deffnm npt -v &", and this nvt_prev.cpt >> file will be used at the beginning of the next step NPT equilibration? >> > >Look at the time stamps. Checkpoint files are mdrun output and are written >per >the mdrun command line -cpt option, which defaults to once every 15 minutes. >A >previous checkpoint (*_prev.cpt) is written as a failsafe, in case something >goes wrong writing the current checkpoint so you don't lose all your work in >the >event of a disruption. > >-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.