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

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