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

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri May 6 14:39:34 CEST 2011

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



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

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