[gmx-users] Exclude the 1-2 and 1-3 interactions

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> By default, Within a same molecule 1-2 and 1-3 interactions does it get
> excluded?

If nrexcl > 2, yes.  The default (pdb2gmx) behavior sets nrexcl=3, but you 
haven't indicated how you generated your topology.

-Justin

> Nilesh
> On Tue, November 9, 2010 10:19 am, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> Hello,
>>> I am working on a system which has a diatomic solute surrounded by water
>>>  molecules. I want to exclude the 1-2 and 1-3 interactions for solute. I
>>> am using OPLS force fild (Gromacs version 4.0.5).
>> If it's diatomic, what 1-3 interactions can it have?  Set nrexcl in the
>> topology accordingly.  That's what it's there for.
>>
>> -Justin
>>
>>
>>> Nilesh
>>>
>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> 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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> 
> 
> 

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

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

========================================