[gmx-users] tpbconv subset

[Justin A. Lemkul]

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.

-- 
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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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