[gmx-users] [gmx-developers] modifying nonbonded interaction parameters

[Justin Lemkul]

I am CC'ing this over to gmx-users because it is not a development question. 
Please post usage questions on gmx-users, not gmx-developers.

On 4/7/14, 9:35 AM, ibrahim khalil wrote:
> dear gromacs users. i am new to gromacs and trying to simulate [multiple]
> carbon nanotubes in water.
> i have a couple of questions-
>
> 1. i was wondering if i can modify the values of σco, εco, σcc, εcc
> parameters in gromacs. i tried to do so by changing the values inside the
> force field file [ffnonbonded.itp] but it does not show expected results. is
> there any way i change those parameters?
>
> 2. i also went through the manual and found the part where it said,
> "changing the Lennard-Jones parameters of an atom type has no effect on
> these combinations". it would be very nice if someone could help me with
> this part.
>

What the manual is saying is that you can change sigma and epsilon however you 
like, and the changes will take effect unless they are overridden by entries in 
[nonbond_params].  If there are no special [nonbond_params] specified for your 
combination of atoms, then the standard combination rules apply.

-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 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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