[gmx-users] extract subset from cpt?

[Justin A. Lemkul]

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

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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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