[gmx-users] extract subset from cpt?

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 18 20:54:34 CEST 2011

Peter C. Lai wrote:
> Is there anyway I can extract a subset of atoms from a cpt file, like I can
> with trjconv operating on a traj file? I want to remove a ligand and still
> keep all the remainder of the state information, so I can feed this back 
> into grompp with a modified topology and "continue" a run without the ligand.

Nope.  For very good reason, too.  If you remove the ligand, you don't preserve 
the state of anything in a meaningful way.  For instance, you're removing 
degrees of freedom from a thermostat (presumably), so you're actually perturbing 
the system, not maintaining it.

The closest you might come would be to dump out your desired group from a .trr 
file and preserve velocities, but you also lose all of the information from the 
.edr file for the reasons described above.



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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