[gmx-users] output force

[Петр Попов]

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?

9 октября 2010 г. 14:50 пользователь Mark Abraham
<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>
> Date: Saturday, October 9, 2010 21:41
> Subject: [gmx-users] output force
> To: 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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