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

Justin A. Lemkul jalemkul at vt.edu
Fri May 6 15:28:13 CEST 2011

Mark Abraham wrote:
> 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.

I've filed a redmine issue for this (http://redmine.gromacs.org/issues/748); it 
looks like the organization of [virtual_sitesn] is different from the other 
[virtual_sites*] directives in terms of the contents.  I think this is why there 
was a "type 7" being detected before.


> Mark
>> 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


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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