Dear all,
Sorry, I realized that. It is just I forgot to delete the pull-coord-init part. But after I delete the followinf lines, ======================================= >> pull-coord1-init = 1.0 >> pull-coord2-init = 1.0 >> pull-coord3-init = 1.0 >> pull-coord4-init = 1.0 >> ============================== and keep the " pull-start = yes " The problem remains. Any new idea on that? Thanks, Yao At 2016-07-07 19:43:54, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 7/6/16 7:24 AM, xy21hb wrote: >> Dear all, >> >> I am pulling the saturated and unsaturated chains of a lipid bilayer to >> "simulate" its gel phase transition by pull code. It ends with the expected >> extended structure. >> >> But when I continue with zero pulling rate >> to maintain the extended structure for a while, the tails go back to the >> original length. >> I guess I have made some mistakes in the mdp pull code part, >> >> ========= >> pull = umbrella >> pull-ngroups = 6 >> pull-ncoords = 4 >> >> pull-group1-name = topC2 >> pull-group2-name = downC2 >> pull-group3-name = topC218 >> pull-group4-name = downC218 >> pull-group5-name = topC316 >> pull-group6-name = downC316 >> >> pull-geometry = distance ; simple distance increase >> >> pull-coord1-groups = 1 3 >> pull-coord2-groups = 1 5 >> pull-coord3-groups = 2 4 >> pull-coord4-groups = 2 6 >> pull-dim = N N Y >> >> pull-coord1-vec = 0 0 1 >> pull-coord1-rate = 0.000 ; 0.01 nm per ps = 10 nm per ns >> pull-coord1-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord2-vec = 0 0 1 >> pull-coord2-rate = 0.000 ; 0.01 nm per ps = 10 nm per ns >> pull-coord2-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord3-vec = 0 0 1 >> pull-coord3-rate = 0.000 ; 0.01 nm per ps = 10 nm per ns >> pull-coord3-k = 1000 ; kJ mol^-1 nm^-2 >> pull-coord4-vec = 0 0 1 >> pull-coord4-rate = 0.000 ; 0.01 nm per ps = 10 nm per ns >> pull-coord4-k = 1000 ; kJ mol^-1 nm^-2 >> >> pull-coord1-init = 1.0 >> pull-coord2-init = 1.0 >> pull-coord3-init = 1.0 >> pull-coord4-init = 1.0 >> >> pull-start = yes ; define initial COM distance > 0 >> >> ============ >> >> Any guess on the reason? Many thanks. >> > >You should use pull-start = yes and not use pull-coord*-init if the lipids are >already in the configuration you want. Otherwise, you're trying to set the >starting distance + 1.0 nm as the reference, which may not be physically >possible or sensible. > >-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.