[gmx-users] output force - 2

[Mark Abraham]

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Wednesday, October 13, 2010 0:50
Subject: Re: [gmx-users] output force - 2
To: Gromacs Users' List <gmx-users at gromacs.org>

> 
> 
> Петр Попов wrote:
> >
> >Is the way to decompose pull force?
> >
> 
> None that I'm aware of.  The only terms that (I think) can 
> be decomposed are short-range nonbonded interactions, using 
> energygrps.
> You might be able to extract forces on subsets of atoms using 
> g_traj, if you've saved forces at suitable intervals (nstfout) 
> in the .trr file.

Maybe, but they won't be forces decomposed group-wise. I've not a clue how the pull force relates to the forces on the atoms, but you can probably get group-wise forces by using mdrun -rerun with well-chosen energy groups, energy group exclusions, and nstfout=1. You will likely need several iterates if you want several decomposed terms.

Mark

> >2010/10/12 Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>>>
> >
> >
> >    Петр Попов wrote:
> >
> >        Hello dear gmx-users!
> >
> >        So, I run md and got 
> all files md.cpt, .trr, .gro, mdf.xvg,... etc.
> >        then I did: grompp_d 
> -f sp.mdp -c md.gro -n index.ndx -p
> >        topol.top -o sp.tpr
> >        where sp.mdp differ 
> from md.mdp in one line: energygrps =
> >        Protein SOL (in 
> md.mdp: energygrps = System)
> >        after that I did: 
> mdrun_d -s sp.tpr -pf spf -rerun md.trr
> >        and got file 
> spf.xvg, but there was no forces:
> >
> >        @    
> title "Pull force"
> >
> >        @    
> xaxis  label "Time (ps)"
> >        @    
> yaxis  label "Force (kJ/mol/nm)"
> >        @TYPE xy
> >        
> 0.000000                0.000000
> >        
> 20.000000               0.000000
> >        
> 40.000000               0.000000
> >        
> 60.000000               0.000000
> >        
> 80.000000               0.000000
> >        
> 100.000000              0.000000
> >        
> 120.000000              0.000000
> >        
> 140.000000              0.000000
> >        
> 160.000000              0.000000
> >        
> 180.000000              0.000000
> >        
> 200.000000              0.000000
> >
> >        Also while reading 
> frame I had a warning:
> >
> >         WARNING: Some 
> frames do not contain velocities.
> >                Ekin, temperature and pressure are incorrect,
> >                the virial will be incorrect when constraints are present.
> >
> >        But I have no idea 
> how to fix this.
> >
> >
> >    I'll take a guess, but that's all it will 
> be.  When using mdrun
> >    -rerun with new energygrps, the only 
> difference is the terms that
> >    are written to the .edr file.  You will 
> not get a different
> >    pullf.xvg file.  The pull force between 
> two groups is independent of
> >    the groups you've set for simple output 
> control, anyway.  That's all
> >    that energygrps will do for you - decompose 
> nonbonded terms between
> >    the selected groups.
> >
> >    Probably the pull code is dependent upon 
> some of the missing terms.
> >     From the warning you get, I suspect 
> that you didn't save velocities
> >    in the .trr file, so some energy terms will 
> be incorrect, as you're
> >    being told.  I doubt, however, that 
> even if you had velocities, the
> >    pullf.xvg file would change.
> >
> >    -Justin
> >
> >
> >        Help me, please.
> >
> >        Sincerely.
> >        Petr.
> >
> >
> >    --     
> ========================================>
> >    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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