[gmx-users] virtual sites

[Gavin Melaugh]

Hi Justin

I am reading the manual at the moment. I want to include some virtual
sites in my molecule so that only surrounding CH3s atom type C3 interact
with then. All other atoms I don't want to interact with them. Do I
create energy groups in the index file called say "virtual sites" and
"exclusions", and list all the indices of the atom types that I don't
want to interact with the virtual site in one group and all the virtual
sites in another.
e.g

[virtual sites]
17 18 19 20

[virtsite_exclus]
1 2 3 4 5 6 7 8 9 .....

Cheers

Gavin

Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Sikandar
>>
>> Cheers. How do you actually define the energy groups?
>>
>
> Read in the manual about the .mdp option "energygrps" and apply custom
> index groups as necessary.
>
> -Justin
>
>> Gavin
>>
>> Sikandar Mashayak wrote:
>>> yes, you can make virtual sites interact with only specific sites by
>>> using Energy Exclusion between energy groups. This can be done by
>>> defining energy groups for virtual sites and other atoms, then exclude
>>> or include the non-bonded interactions between them accordingly...
>>>
>>> On Thu, May 5, 2011 at 7:30 AM, Gavin Melaugh <gmelaugh01 at qub.ac.uk
>>> <mailto:gmelaugh01 at qub.ac.uk>> wrote:
>>>
>>>     Hi All
>>>
>>>     Is it possible to have a virtual site interact with only specific
>>>     atoms
>>>     and not interact at all with everything else?
>>>
>>>
>>>     Cheers
>>>
>>>     Gavin
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>>
>