[gmx-users] water handling
ksr at chemistry.umass.edu
Tue Mar 9 21:03:00 CET 2004
Thanks, but perhaps I wasn't sufficiently clear as to my needs. Your
method requires an "index.ndx" file containing the index of the atoms
in my protein as well as the "N waters that are closest to the
protein". However, I was effectively wondering how to generate this
index, i.e. I do not know, a priori, what waters are close to the
protein, I was hoping to map them somehow w/in GROMACS (e.g.
retain/report solvent molecules XÅ from a protein atom) and use your
method to then remove all the bulk water retaining only those close to
On Tuesday, March 9, 2004, at 11:40 AM, Nguyen Hoang Phuong wrote:
> On Tue, 9 Mar 2004, Ken Rotondi wrote:
>> I've run some trajectories in explicit solvent. I'd like to observe
>> 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
>> 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,
>> 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
> protein and N waters which are closest to the protein.
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The Gierasch Laboratory
The University of Massachusetts-Amherst
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