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

Justin A. Lemkul jalemkul at vt.edu
Fri May 6 14:10:15 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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