[gmx-users] solvent atom numbers

[Y. U. Sasidhar]

Giorgos Karvounis wrote:

>Dear all,
>
>i have this little problem with solvent atom numbers. I want to do some
>analysis of water molecules (e.g. the lifetime of specific water
>molecule(s) close to hydrogen bond )  and so i want to find out which of
>the water molecules of the box stay within a certain distance from the
>c.o.m of my peptide. Using trjorder, i create a xtc file but with the
>rearanged molecules, i can find how many of the water molecules are
>within that distance but this doesnt tell me which of the water
>molecules of the original run belong to that distance. g_mindist tells
>me the number of contacts (and min_distance) but not the atom-number.
>So, at the end i am not sure of which atoms (water molecules) to
>analyse.I hope this makes sense.
>
>Thanks
>
>Giorgos
>
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>  
>
you may try g_dist with -dist option. That will give an output which can 
be redirected to a file for analysis.
The output will have sol ids,atomids etc.

-- 
 Sasidhar