[gmx-users] water handling

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Tue Mar 9 17:42:01 CET 2004

On Tue, 9 Mar 2004, Ken Rotondi wrote:

> Hello,
> I've run some trajectories in explicit solvent. I'd like to observe the
> behavior of the water molecules in the first several layers of solvent
> around the protein. Is there any way in the GROMACS package that I can
> strip away the bulk water and look at snapshots of just the protein and
> its associated waters? I've looked through trjconv but did not see a
> solution to my need.
> As always, thanks in advance for any help,
> Ken
> K.S.Rotondi
> Research Associate
> The Gierasch Laboratory
> The University of Massachusetts-Amherst

you can use trjorder and trjconv for your need.

trjorder -f xxx.trr -s xxx.tpr -o xxx_order.trr

trjconv_d  -f xxx_order.trr -s xxx.tpr -n index.ndx -o yyy.gro

where index.ndx is the index file containning the index of atoms of your
protein and N waters which are closest to the protein.


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