Hi Justin I am reading the manual at the moment. I want to include some virtual sites in my molecule so that only surrounding CH3s atom type C3 interact with then. All other atoms I don't want to interact with them. Do I create energy groups in the index file called say "virtual sites" and "exclusions", and list all the indices of the atom types that I don't want to interact with the virtual site in one group and all the virtual sites in another. e.g
[virtual sites] 17 18 19 20 [virtsite_exclus] 1 2 3 4 5 6 7 8 9 ..... Cheers Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Sikandar >> >> Cheers. How do you actually define the energy groups? >> > > Read in the manual about the .mdp option "energygrps" and apply custom > index groups as necessary. > > -Justin > >> Gavin >> >> Sikandar Mashayak wrote: >>> yes, you can make virtual sites interact with only specific sites by >>> using Energy Exclusion between energy groups. This can be done by >>> defining energy groups for virtual sites and other atoms, then exclude >>> or include the non-bonded interactions between them accordingly... >>> >>> On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh <gmelaug...@qub.ac.uk >>> <mailto:gmelaug...@qub.ac.uk>> wrote: >>> >>> Hi All >>> >>> Is it possible to have a virtual site interact with only specific >>> atoms >>> and not interact at all with everything else? >>> >>> >>> Cheers >>> >>> Gavin >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto: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 >>> <mailto:gmx-users-requ...@gromacs.org>. >>> Can't post? Read 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