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

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri May 6 13:54:29 CEST 2011


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

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

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