[gmx-users] water handling

[Nguyen Hoang Phuong]

On Tue, 9 Mar 2004, Ken Rotondi wrote:

> Phuong/all,
>
> 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
> the protein.
if you need N_water water molecules those are closest to the protein then
the index file look like:

[ atoms ]
1
2
3
4
.
.
.
N_protein
N_protein +1
N_protein +2
.
.
.
3*N_water

where N_protein is the number of atoms of your protein. You can play with
the value of N_water to get to know how many waters you need. For example,
my protein has 5 atoms and I would like to see only 2 nearest waters at
every time step then first I use trjorder to order my trajectory and then
use the trjconv with the index file:

[ atoms ]
1
2
3
4
5
6
7
8
9
10
11

You need 5 + 3*2 = 11 numbers in this file.

Phuong