[gmx-users] virtual sites set up for topology file

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri May 6 14:17:29 CEST 2011

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

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