On 2/5/14, 2:10 PM, Xu Dong Huang wrote:
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?
nrexcl = 3, as explained in the manual.
-Justin
Thanks,
On Feb 2, 2014, at 11:31 AM, Justin Lemkul <[email protected]> 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
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201
[email protected] | (410) 706-7441
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==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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