For doing that you first tag only those water molecules which are within 0.5nm of the protein surface throughout the trajectory. To do it you need to write a small python script using common_member option. And make an index file only with those water molecules and calculate the rdf.
On Wed, 28 Aug 2019, 2:45 pm anupama sharma, <anusharma.jan1...@gmail.com> wrote: > Dear users, > I have to calculate the Pair Distribution Function of water present in my > system near protein surface at 5 angstorm region for which I already did > the indexing using gmx select (dynamic indexing). But when I tried to > calculate the Pair Distribution Function using gmx rdf, I am getting option > as to select the reference "the atoms present in one frame", not the > atom/molecule for the system within a defined region and hence, I am unable > to calculate the RDF of water molecule within a defined region for the > whole trajectory which I want to do. Is there any possibility in gromacs to > do so. I'll highly greatful if any one can help. > > Thanks in advance > With regards, > Anupama > -- > 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.