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

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri May 6 15:30:14 CEST 2011

Hi Mark

Many thanks to you and all your colleagues for replying. This has
worked, at least there are now no errors. Where the manual is incorrect
is that it leads you to believe that you state;
[virtual _siten]
;index of VS  index of atoms for COG  func
                229     8 11 15                            1

However the function type should be stated before the atom indices
comprising the COG
;index of VS  func     indices
   229                  1           8 11 15             



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.
> 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

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