[gmx-users] output force - 2

[Петр Попов]

Is it possible to slightly change the source code to adjust output of
pullf in appropriate form? And if it is, how?

Petr.

12 октября 2010 г. 17:49 пользователь Justin A. Lemkul
<jalemkul at vt.edu> написал:
>
>
> 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.
>
> -Justin
>
>> 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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