Hi Mark Cheers.Could you perhaps shed some insight into format of [virtual_siten] when trying to define the VS at the COG of three atoms. It is not obvious from the manual
Cheers Gavin Mark Abraham wrote: > On 6/05/2011 10:17 PM, Gavin Melaugh wrote: >> 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. > > Yes it does, but (IIRC) the implementation requires that each of the > constructing atoms and the virtual atom(s) are distinct atoms. mdrun > does the book-keeping to know which atoms are sensible at different > stages of the integration. So the input coordinate file needs to have > such atoms there, but I rather suspect their coordinates will get > ignored - that's easily tested, of course. > > Mark > >> 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 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
