[gmx-users] output force

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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.abraham at anu.edu.au <mailto:mark.abraham at anu.edu.au>
>         <mailto:mark.abraham at anu.edu.au
>         <mailto:mark.abraham at 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 <magistrpetrus at gmail.com
>         <mailto:magistrpetrus at gmail.com>
>            <mailto:magistrpetrus at gmail.com
>         <mailto:magistrpetrus at gmail.com>>>
>            Date: Saturday, October 9, 2010 21:41
>            Subject: [gmx-users] output force
>            To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>         <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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

========================================