Hi Stephane, The map shows weather a certain hydrogen bond exists at a certain time. In principle you can get the information by integrating this data, but I'm not sure it can be done without changing the code. A possible solution is to use a script and run g_hbond -num 28 times with two relevant groups (N-H donor and oxygen acceptor), and calculate the occupancy based on this (I guess you mean the fraction of time that this h_bond existed.
Ran. ABEL Stephane 175950 wrote: > Hi everybody, > > I am doing some analysis of the interpeptidique hbonds (INTRHB) during the > aggregation in beta fuof 4 heptapeptides in water > > I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the > 28 INTRHB like this > > NH--CO > > > [intra_hbds] > 4 17 5 > 18 26 19 > 27 43 28 > 44 52 45 > 53 60 54 > .... > > to obtain the INTRHB existence map i used the command with gmx4.05 > > g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f > ./XTC/Whole_Traj_53A6Center.xtc -b 400000 -e 500000 -hbn > 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map > > The map show in the x and y axis the time and residue (up to 84). I have no > idea what the figure means. The olot is stored here > http://www.st-abel.com/Hbond_occupency.jpg > > I want only to know if, for example, the Hbond_occupency for the group NH or > CO of the residu 1 > > Thank you in advance for your help > > Stephane > -- 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