Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist.
Hope that helps, Ran. Rasmus "Termo" Lundsgaard wrote: > Hi All. > > I'm trying to calculate the Hydrogen bond occupancy when there is two > hydrogen bonds between same two acetic acid molecules at the same time. > > With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen > bonds" group and the hbmap.xpm gives me the matrix of when these > hydrogen bonds exist for each timeframe... > > How can I calculate the occupancy of when two hydrogen bonds exist > between the same two molecules?? > > > Best regards > Rasmus -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
