[gmx-users] stripping water

Ken Rotondi ksr at chemistry.umass.edu
Tue Oct 11 17:25:30 CEST 2005

Hello all,

This is a repost of a dead thread. At the time it was rather esoteric, 
however, data piling up has made it a more urgent matter...

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, and these will certainly change over the course of a 
simulation. I was hoping to order them in GROMACS using trjorder, and 
subsequently strip away all but the closest (i.e. early in the ordered 
trajectory) x (say 300) solvent molecules.


 >> 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 
 >> around the protein. Is there any way in the GROMACS package that I 
 >> 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
 > 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.
 > Phuong
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