Hi Justin I do not intend to have charges on the sites. All I want is; when a CH3 group gets close to the site it feels a repulsive force. I have calculated a sigma and epsilon value for this interaction.
Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> 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 ..... >> > > In a general sense, yes, that's the right approach. Note that if any > of these sites is charged and/or you're using PME, then this whole > exclusion thing goes out the window, as has been discussed several > times in recent days. Using energygrp_excl applies only to > short-range nonbonded interactions. If you need complete exclusion, > you may have to look into tabulated potentials if this is the case. > > -Justin > -- 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