Hi Sikandar Many Thanks for the reply. When you define energygrps in the mdp file, does that mean that only these groups are written to the energy file. I take it that all iother information regarding the energy is written as well i.e if you left this section blank
Cheers Gavin Sikandar Mashayak wrote: > you can do it as following > > 1. create index file make_indx -f conf.gro -n index.ndx ( select VS > and any other atoms you want lets say OTHERS) > 2. in .mdp define energygrps "VS OTHERS" > 3. exclude interactions by specifying energygrp_excl VS OTHERS in .mdp > file > > for more you can refer to manual.. > > I hope it helps > > -- > sikandar > > > > On Thu, May 5, 2011 at 11:00 AM, Gavin Melaugh <gmelaug...@qub.ac.uk > <mailto:gmelaug...@qub.ac.uk>> wrote: > > Hi Sikandar > > Cheers. How do you actually define the energy groups? > > 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> > > <mailto: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> > > <mailto: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> > > <mailto: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 > <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
