[gmx-users] Umbrella Sampling-gmx distance

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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