in doing so .. by default all pair interactions with virtual sites would result in zero forces except those between atoms defined in [nonbond_params]
On Thu, May 5, 2011 at 11:57 AM, Sikandar Mashayak <symasha...@gmail.com>wrote: > hey > > another approach to do this without using energy group exclusion is to > define non-bonded interactions parameter explicitly between atoms in > ffnonbonded.itp file. You can specify sigma and epsilon to be zero in > virtual sites atoms definition and specify individual pair interactions > parameters using non-bonded interactions like following ... > > ; virtual site > VS1 0 0 0 D 0 0 > VS2 0 0 0 D 0 0 > VS3 0 0 0 D 0 0 > > [ nonbond_params ] > VS1 C 1 1.0 0.25 > VS2 C 1 1.0 0.25 > VS2 C 1 1.0 0.25 > > -- > sikandar > > On Thu, May 5, 2011 at 11:47 AM, Gavin Melaugh <gmelaug...@qub.ac.uk>wrote: > >> 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 >> > >
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