[gmx-users] output force

[Justin A. Lemkul]

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>> 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>>
>     Date: Saturday, October 9, 2010 21:41
>     Subject: [gmx-users] output force
>     To: 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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> 

-- 
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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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