Dear Justin,
Will you please write out the restart command for me? I am afraid without your written command I cannot do it. Brett At 2016-04-05 22:06:57, "Justin Lemkul" <[email protected]> wrote: > > >On 4/5/16 10:04 AM, Brett wrote: >> Dear Justin, >> >> WIll you please give a reply for the following question? Most probably I >> need to restart my MD from the beginning? >> > >Restart from the last checkpoint and use -cpi -append. mdrun will overwrite >the >broken frames. No need for trjcat, trjconv, etc. > >-Justin > >> Brett >> >> >> >> >> >> >> >> At 2016-04-05 17:18:31, "Brett" <[email protected]> wrote: >> >> Dear All, >> >> >> After energy minimization and equilibration, I started a 10 ns production >> MD. By accident the production MD stopped at 450 ps (which produced >> md_0_1.trr), and I continue the production MD from the previous 450 ps point >> (which produced md_0_1_from0.45to10ns.trr). >> >> >> Then by gmx trjcat -f md_0_1.trr md_0_1_from0.45to10ns.trr -b 2330 -e 2331 >> -o md_0_12330psto2332ps.trr, I tried to get 2330-2331 frame trr file. >> However although I got the md_0_12330psto2332ps.trr, GROMAS gave a strong >> warning message: >> WARNING: Incomplete frame: nr 234 time 468 >> >> >> Will you please advise whether my " md_0_1_from0.45to10ns.trr" was totally >> broken and whether I need to restart my production MD? And why I got the >> incomplete frame? >> >> >> Brett >> >> >> >> >> >> >> >> > >-- >================================================== > >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]. -- 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].
