[gmx-users] output force

[Петр Попов]

So if I want to get protein-solvent component I should add in .mdp:

energygrps = Protein SOL

?

10 октября 2010 г. 16:41 пользователь Justin A. Lemkul <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>> 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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> --
> ========================================
>
> 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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