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

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 6 15:22:09 CEST 2011

On 6/05/2011 10:39 PM, Gavin Melaugh wrote:
> 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

Indeed, it's undocumented - but I think Sikander's experience from my 
discussion in this thread earlier this month 
http://lists.gromacs.org/pipermail/gmx-users/2011-May/060994.html should 
point the way for you.


> 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

More information about the gromacs.org_gmx-users mailing list