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: https://extras.csc.fi/chem/courses/gmx2004/exercises/index.html 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? best, Olga
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