I want to pull a carbon particle (170 atoms in a lattice) across an interface between Liquid A and Liquid B. The particle starts out in Liquid A with the center of mass at about x = 2.5 y = 2.5 z = 2.5. The liquid-liquid interface is at about z = 5. I want to pull the particle in a straight line in the positive z direction. So I put a dummy atom (no interaction perameters) in Liquid B at x = 2.5 y = 2.5 z = 7.5 to use as a reference. I put the dummy atom in a freeze group to keep it from moving. This is my pull code in my .mdp file, plus the freeze group code (DMY is the dummy atom, DNP is the carbon particle):
; Pull code pull = umbrella pull_geometry = distance ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = DMY pull_group1 = DNP pull_rate1 = -0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 ; Define dummy atom as freeze group freezegrps = DMY freezedim = Y Y Y At first I used a negative pull rate because this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html ) says to use a negative pull rate if you want to decrease the distance between pull_group0 and pull_group1. But instead of moving in a straight line in the positive z direction, the particle moved in the negative z direction at an angle (could this be because of periodic boundary conditions?) When I tried to use a positive pull rate the particle just shuffled around in a little x-y circle. What am I doing wrong? -- 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.