Re: selectively write atom coordinates on-the-fly

From: Joshua Adelman (
Date: Thu May 21 2009 - 11:41:11 CDT

As far as I know, you cannot selectively write a subgroup of atoms to
the dcd file during a simulation. You can certainly strip away the
waters later, either using catdcd or a number of other methods.


On May 21, 2009, at 9:29 AM, Vasudevan V wrote:

> Hello All,
> I was wondering if it is possible to selectively write the
> coordinates of certain groups while running a simulation.
> For example if i want to write only the protein coordinates to the
> dcd and not the water coordinates.
> In gromacs you can do that by selecting the xtcgroups in the run
> parameters file(.mdp).
> regards
> vasu

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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