Yeah I see your point about the types. With regard to the initial configuration state I would have assumed that gromacs knew the initial position of the virtual site when I stated that it was to be at the COG of the 3 atoms in the [virtual_sitesn] directive.
Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Justin >> >> I have tried this but I am now getting different errors. I take it that: >> I specify the virtual sites in the atomtypes directive as I have seen >> from examples? > > Virtual sites are included in all the force fields already, but if you > want some custom name, then yes, include them in a new [atomtypes] > directive. I see no reason to create three distinct, but identical, > types as you have. > >> I index the virtual sites in the atoms directive in accordance with the >> rest of the molecule. atom numbers go from 1-228, therefore I label the >> 3 virtual sites 229 to231. >> The error I get now is >> >> Atom index (229) in virtual_sites3 out of bounds (1-228). >> This probably means that you have inserted topology section >> "virtual_sites3" >> in a part belonging to a different molecule than you intended to. >> In that case move the "virtual_sites3" section to the right molecule. >> >> Do I have to have the virtual sites in the gro file also? This doesn't >> make sense >> > > Yes, you need their coordinates as part of the initial state. > > -Justin > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
