[gmx-users] the relationship between mdp file and the force field

[Justin Lemkul]

On 4/26/15 10:17 PM, Brett wrote:
> Dear All,
>
> In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific force field OPLS-AA force field. It specifically mentioned "Settings, particularly nonbonded interaction settings, will be different for other force fields".
>
> Will you please introduce to me how to modify mdp files based on the difference of the force fields? For example, if I use force field 6, what should I modify based on the mdps of the lysozyme tutorial?
>
> I am looking forward to getting your reply.
>

"Force field 6" is not very precise, because the numbering in the pdb2gmx list 
varies between GROMACS versions.  What force field (exactly) are you using? 
Have you read the primary literature for the force field?  Settings are given in 
the parametrization/validation papers and that's what you should use.

-Justin

-- 
==================================================

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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