On 1/11/18 3:43 AM, rose rahmani wrote:
Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp file for pulling: integrator = md dt = 0.001 nsteps = 2500000 nstxout = 5000 nstvout = 5000 nstfout = 500 nstlog = 500 nstenergy = 1000 nstxtcout = 1000 nstlist = 10 rlist = 1.5 cutoff_scheme = group coulombtype = pme rcoulomb = 1.5 vdwtype = Switch rvdw_switch = 1.0 rvdw = 1.2 pcoupl = no gen_vel = no constraints = h-bonds ns_type = grid pbc = xy freezegrps = WAL ZnS freezedim = Y Y Y Y Y Y energygrp-excl = WAL WAL ZnS ZnS energygrps = SOL WAL ZnS Protein NA CL nwall = 2 wall-atomtype = C C wall-type = 9-3 wall-density = 150 150 wall-ewald-zfac = 3 ewald-geometry = 3dc fourierspacing = 0.12 tcoupl = v-rescale tc-grps = System tau-t = 0.1 ref-t = 300 ; Pull code pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = ZnS pull_group2_name = Protein pull_coord1_type = umbrella pull_coord1_geometry = direction pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_vec = 0 0 1 pull_coord1_rate = -0.001 pull_coord1_k = 5000 pull_coord1_start = yes pull_nstxout = 10 and this is dist0.xvg # This file was created Thu Jan 11 03:19:07 2018 # Created by: # :-) GROMACS - gmx distance, VERSION 5.1.4 (-: # # Executable: /usr/local/gromacs/bin/gmx # Data prefix: /usr/local/gromacs # Command line: # gmx distance -s pull.tpr -n index.ndx -f conf0.gro -oall dist0.xvg
By using -oall, you're getting a matrix of all distances between the atoms in the selected groups. You just want a COM distance, so you need -oxyz with a suitable COM selection (see http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-dist)
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
