[gmx-users] tpbconv subset

[John Shultz]

Justin,

Only problem is I need to change this parameter
energygrps

to track the energy on specific groups in the simulation. Is there a
way to modify the simulation parameters to track these energies?

On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> John Shultz wrote:
>>
>> I want to run a subset of an original trajectory. I know how to get
>> the tpr consisting of the subset. How do I modify the simulation with
>> a new mdp file and then run the mdrun? I was referencing these
>> instructions
>>
>
> If you have a .tpr file, then the .mdp file is a step backwards.  You don't
> need it.
>
> Assuming you want to do some sort of re-run procedure, you simply have to
> run:
>
> mdrun -s subset.tpr -rerun original.xtc
>
> (where original.xtc is your trajectory file that contains the same subset of
> atoms as subset.tpr)
>
> -Justin
>
>> http://manual.gromacs.org/current/online/tpbconv.html
>> 3nd. by creating a tpx file for a subset of your original tpx file,
>> which is useful when you want to remove the solvent from your tpx
>> file, or when you want to make e.g. a pure Ca tpx file. WARNING: this
>> tpx file is not fully functional.
>
> --
> ========================================
>
> 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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