Any comment on this would be so appreciated! Regards, Alex
On Sat, Apr 18, 2020 at 2:12 PM Alex <alexanderwie...@gmail.com> wrote: > Dear all, > To generate the initial configurations for umbrella sampling, I conducted > a simple pulling simulation by which a single-small molecule (mol_A) is > being dragged along -Z from water into the body of a thin film. > Since the thin film is large I used *"pull-pbc-ref-prev-step-com = yes" > and "pull-group1-pbcatom = -1"* which cause a net shifting of the > system along the pulling direction as soon as the mol_A reach to the thin > film, please find below the pulling flags movie and plot in below links. > > Centering the thin film and mol_A could solve the issue, (echo 1 0 | > trjconv -center yes) to some extent but still COM changes in the early > stage below 2ns. , > COM: > https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0 > > Movie in which the water molecules are hidden: > https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv > > - > gmx version 2020.1 > ----- > pull = yes > pull-print-com = no > pull-print-ref-value = yes > pull-print-components = Yes > pull-nstxout = 1000 > pull-nstfout = 1000 > pull-pbc-ref-prev-step-com = yes > pull-ngroups = 2 > pull-ncoords = 1 > pull-group1-name = Thin-film > pull-group1-pbcatom = -1 > pull-group2-name = mol_A > pull-group2-pbcatom = 0 > pull-coord1-type = umbrella > pull-coord1-geometry = direction > pull-coord1-groups = 1 2 > pull-coord1-dim = N N Y > pull-coord1-origin = 0.0 0.0 0.0 > pull-coord1-vec = 0.0 0.0 -1.0 > pull-coord1-start = yes > pull-coord1-init = 0 > pull-coord1-rate = 0.0005 > pull-coord1-k = 5000 > ----- > I wonder if I could extract correct initial configuration from this > trajectory? With correct initial configuration, I mean a set of gro file in > which change from one from to another is the distance between the COM of > the thin-film and mol_A? > > Thank you > Alex > -- 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.