[gmx-users] Umbrella Sampling-gmx distance
Justin Lemkul
jalemkul at vt.edu
Thu Jan 11 15:52:29 CET 2018
On 1/11/18 9:50 AM, rose rahmani wrote:
> still like this
You're not using the command syntax shown in the link I provided.
-Justin
> # This file was created Thu Jan 11 09:46:46 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 -n index.ndx -f conf0.gro -oxyz dist0.xvg
> # gmx distance is part of G R O M A C S:
> #
> #
> ¸<8d><9e><89><9a><93>ÃÂ<8a><9d><8c>ð<99><8b><9a><91>ò<9e><91><86>þ<88><99><8a><93><93><86>ü<9e><8a><8b><9a><8d><96><85><9ì<90><8d><9a><8c>
> #
> @ title "Distance"
> @ xaxis label "Time (ps)"
> @ yaxis label "Distance (nm)"
> @TYPE xy
> 0.000 0.192 0.270 0.191 -0.192 -0.270 0.191 0.383
> 0.000 0.000 0.383 0.000 0.000 0.383 0.000 0.000
> 0.383 0.000 0.000 1.131 0.270 0.191 0.382 0.000
> 0.000 0.382 0.000 0.000 0.383 0.000 0.000 0.383
> 0.000 0.000 0.383 0.000 0.000 0.383 0.000 0.000
> 0.383 0.000 0.000 0.382 0.000 0.000 0.748 -0.270
> 0.191 0.382 0.000 0.000 0.382 0.000 0.000 0.382
> 0.000 0.000 0.382 0.000 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.192 0.270 0.191
> -0.192 -0.270 0.191 0.383 0.000 0.000 0.383 0.000
> 0.000 0.383 0.000 0.000 0.383 0.000 0.000 1.131
> 0.270 0.191 0.382 0.000 0.000 0.382 0.000 0.000
> 0.383 0.000 0.000 0.383 0.000 0.000 0.383 0.000
> 0.000 0.383 0.000 0.000 0.383 0.000 0.000 0.382
> 0.000 0.000 0.748 -0.270 0.191 0.382 0.000 0.000
> 0.382 0.000 0.000 0.382 0.000 0.000 0.382 0.000
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.541 0.000 0.000
> 0.541 0.000 0.000 0.541 0.000 0.000 0.541 0.000
> 0.000 0.541 0.000 0.000 0.541 0.000 0.000 0.541
> 0.000 0.000 0.541 0.000 0.000 0.
>
>
>
> On Thu, Jan 11, 2018 at 4:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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/docu
>> mentation/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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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