[gmx-users] (no subject)

[Justin Lemkul]

On 6/28/15 3:22 PM, Vidyalakshmi CM wrote:
> Hi,
>
> You may use the mdp files from the tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
> (It has topologies for energy minimzation, nvt and npt simulations and md
> simulations run).
>

The tutorial .mdp settings are for OPLS-AA and may not be generally applicable 
to any other force field.  This is a non-trivial consideration in running 
simulations properly.

"AMBER force field" is a bit generic; different parameter sets use subtly 
different parameters.  The primary literature for the parameter set of interest 
will contain the proper run settings.  Use whatever those settings are.

-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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