[gmx-users] virtual sites

[Justin A. Lemkul]

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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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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