[gmx-users] interaction potential parameters Between H2O And CO2

[Justin Lemkul]

On 9/14/15 2:26 AM, Zhongjin He wrote:
> Dear  Justin,
>
>
> Thanks for you reply. I have set up it
>
>
> [ nonbond_params ] ; i j func sigma epsilon OW_ice CZ 1 0.31156 0.293002 OW_ice OZ 1 0.30297 0.532092 HW_ice CZ 1 0.28142 0.299728 HW_ice OZ 1 0.21942 0.392318
>
>
>  From the GROMACS manual, I find for [ nonbond_params ], func 1 means using LJ and func 2 means using Buckingham.
> In my case, LJ is used. But I am a little confused that whether sigma and epsilon are directly used in [ nonbond_params ]
> or 4* epsilon*sigma^6 and 4* epsilon*sigma^12 are used in [ nonbond_params ]?
>

OPLS-AA uses comb-rule 3 in [defaults], so this means sigma and epsilon directly 
(see manual section 5.3.2)

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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