On Mar 14, 2014 4:27 AM, "virk" <virkbl...@yahoo.com> wrote: > > Dear Justin, > > Thanks for feedback...The percentage of glycine molecules that > exist as monomers (i.e., with no hydrogen bonding to any > other glycine molecule), dimers (i.e., pairs of glycine > molecules hydrogen bonded to each other but not to any other > glycine molecule), and trimers (i.e., groups of three glycine > molecules hydrogen bonded to each other but not to any other > glycine molecule).
Now you have definitions that can be implemented (whether they are the right definitions is your call). Unfortunately, they are complex. Identifying putative dimers is straightforward, but pruning the list of higher-order associations requires identifying that each member of a putative dimer is a member of no other dimer. g_select is good for the former (but you probably have to define a hydrogen bond criterion yourself), but I don't know if it can do the next stage, even in a second call. If not, then you will need to write a script - which you would need anyway if you were to try to use g_hbond. Mark > I am using default h-bond criteria 0.35 nm but that can > be changed accordingly. > > Amninder virk > > -- > View this message in context: http://gromacs.5086.x6.nabble.com/h-bonds-tp5015132p5015142.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.