[gmx-users] Bond interaction exclusions

[Justin Lemkul]

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

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

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