[gmx-users] solvent atom numbers

Y. U. Sasidhar sasidhar at chem.iitb.ac.in
Tue Feb 11 04:05:46 CET 2003

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.
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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.


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