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? 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 Gavin Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> Hi Justin >> >> Thanks for the reply. To create a virtual site at the centre of geometry >> of 3 atoms, according to the manual, do you not say: [virtual_sitesn], >> the index of the site, the index of the three atoms and then the >> function type 1 which determines that it is COG. > > OK, so that would seem to be right from Table 5.6, but it's not > discussed anywhere else, so I suspect that it may be a feature that > either got broken along the way, or for some other reason doesn't > work, since it's not :) > >> Or as I now realise. State [virtual_site3], site index atom indices, and >> function 1. The fact that there are no parameters then by default must >> mean it is COG. Is this correct? >> > > I don't know if [virtual_sites3] can be specified without any > parameters. It seems to me that this shouldn't be correct. It never > hurts to try. > > -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
