[gmx-users] tpbconv subset

Justin A. Lemkul jalemkul at vt.edu
Sun May 23 23:07:19 CEST 2010

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)


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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