[gmx-users] water residence time on a certain group of ligand

Olga Ivchenko olga.ivchenko at gmail.com
Wed Mar 2 10:52:57 CET 2011

Dear gromacs users,

I want to calculate water molecules residence time on a certain groups of a
ligand. I found in gromacs exercises how to do it:
To get water residence time I need:
1) Obtain hbac.xvg, using this command:  g_hbond -contact -n index -ac -r
0.6 -b 200
2) Integrate with g_analyze S0 and S1 (I am not quite sure S1 or S0).

I used the command:  g_hbond -contact -b 100 -nomerge -r 0.35 -f
traj-prod315k.xtc  -s prod.tpr -n index.ndx

But I can not get the correct number of contacts with this command, because
the output is : Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.4#
Average number of contacts per timeframe 0.000 out of 612 possible

-Is that mean that there is a zero contacts within a certain distance?

I do not know is it does make sense to integrate So and S1 after using the
command:  g_hbond -contact -b 100 -nomerge -r 0.35 -f traj-prod315k.xtc  -s
prod.tpr -n index.ndx, because the program produce hbac.xvg file, but writes
that no contacts were found.

Please could you advice me on this?

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