[gmx-users] Bond interaction exclusions

[Justin Lemkul]

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

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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