[gmx-users] Bond interaction exclusions
Xu Dong Huang
xudonghmath at gmail.com
Wed Feb 5 20:10:33 CET 2014
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?
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
>> ;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 A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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