[gmx-users] problem with pull code

[xy21hb]

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-start = yes ; define initial COM distance > 0 >> >> ============ >> >> Any guess on the reason? Many thanks. >> Yao -- 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-request at gromacs.org.