Sir, I used gromacs 4.6. I got the point - index file will tell how many contacts an atom has made during the trajectory. Whether it has made a contact with an atom only in once or all the time, in the whole trajectory, it will be mentioned. Am I right?
So from the problem I had, can I say that no. of contact/atom had increased in S2 while the no. of contact/time decreased? Its a bit confusing though! Thank you kavya On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > To clarify: the -hbn output is not very indicative of how many contacts > there were since some of them could be present in one frame but absent in > 999999. The -num option, however, provides the number of contacts over > time, and its time average probably tells you much more in this case. > > What version of g_hbond are you using? I remember there were several > bugfixes over the last 6 months or so. With the latest version(s) I believe > that the -merge flag has no effect on contact analysis, which is correct. > > Erik > > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
