Thank you Sir. On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote:
> > On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote: > > 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? >> > > Yes. > > > >> 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? >> > > That depends. If 'contact' means unique interactions and 'atom' means e.g. > all atoms in in your system, then yes. > > >> 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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
