Петр Попов wrote:
So if I want to get protein-solvent component I should add in .mdp:
energygrps = Protein SOL
?
Yes, and set nstlist = 1.
-Justin
10 октября 2010 г. 16:41 пользователь Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> написал:
Петр Попов wrote:
Thank you for response!
One more question:
How can I get file with energy groups? Should I use grompp with
a -e ener.edr option? In this case, how to build ener.edr file?
The "energrygrps" keyword is an .mdp option, so generate a new .tpr
file with the desired groups and use the -rerun feature of mdrun on
the trajectory that has already been produced.
-Justin
9 октября 2010 г. 14:50 пользователь Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>> написал:
You can get that with cunning use of energy groups and mdrun
-rerun,
but not mid-simulation.
Mark
----- Original Message -----
From: Петр Попов <magistrpet...@gmail.com
<mailto:magistrpet...@gmail.com>
<mailto:magistrpet...@gmail.com
<mailto:magistrpet...@gmail.com>>>
Date: Saturday, October 9, 2010 21:41
Subject: [gmx-users] output force
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
> Hello dear gmx-users!
>
> When calculated forces in gromacs to produce pmf, we have
the net
force in output. For example:
> ...
> #
> # Giving Russians Opium May Alter Current Situation
> #
> @ title "Pull force"
> @ xaxis label "Time (ps)"
> @ yaxis label "Force (kJ/mol/nm)"
> @TYPE xy
> 0.000000 1017490.761270
> 0.002000 -253098.034916
> 0.004000 -43856.400160
> 0.006000 48980.619113
> 0.008000 52103.053067
> 0.010000 33788.090031
> 0.012000 19096.388350
> 0.014000 14094.738810
> 0.016000 14027.621966
> 0.018000 15162.993741
> 0.020000 14136.978177
> ... etc.
>
> What sould I do to get the net force of protein-solvent
interactions or protein-protein interactions or solvent-solvent
interactions instead and get output .xvg file in the form
like this:
>
> time Force(type1) Force(type2) Force(type3)
>
> t1 f1 f1 f1
> t2 f2 f2 f2
> t3 f3 f3 f3
> ... ... ... ...
> etc.
>
> Thank you for attention and I hope you will help me!
> --
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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