[gmx-users] Bond interaction exclusions

[Xu Dong Huang]

Thank you for the information, I wish to exclude 1-3 and 1-4 interactions in my simulation, therefore how would I change my topology to achieve this effect if I want to turn both 1-3 and 1-4 off? 

Thanks,

On Feb 2, 2014, at 11:31 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> On 2/2/14, 11:29 AM, Xu Dong Huang wrote:
>> Dear all,
>> 
>> I am unclear about the bond exclusion properties within gromacs. Using a martini model system, what is the default behavior of setting
>> [moleculetype]
>> ;name	exclusions
>> eth      1
>> 
>> exclusions to 1? How do I find out what kind of interaction it is excluding? I am interested in finding out if this is excluding 1-3 interaction or 1-4 interaction. I guess what I also want to know is if my settings are including 1-4 bonded interactions or using only 1-3.
>> 
> 
> The value of nrexcl is the number of bonded neighbors that are excluded from nonbonded interactions.  With nrexcl = 1, only 1-2 interactions are excluded; 1-3 and 1-4 interactions are calculated as normal nonbonded interactions.
> 
> -Justin
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> 
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