[gmx-users] output force
Петр Попов
magistrpetrus at gmail.com
Sun Oct 10 18:01:09 CEST 2010
Thank you very much!
10 октября 2010 г. 19:58 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:
>
>
> 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
>
> ========================================
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