[gmx-users] mdp file

[Justin Lemkul]

On 9/1/15 12:50 PM, Sotirios Dionysios I. Papadatos wrote:
> Hi,
>
> I am having some trouble defining a proper mdp file for minimization and production runs. I am aware of the manual's - site's reference to this matter, it is pretty thourough.
>
> My question is: How do I know which parameters to use for each simulation? Is there a publication, book etc to guide the user through this? I mean for example if I want to simulate a protein, which parameters do I have to use??
>

Try some tutorials.

http://www.gromacs.org/Documentation/Tutorials

Most settings (output, thermostats, etc) are pretty boilerplate.  The nonbonded 
setup (cutoffs) depend on the force field, which you will learn about by reading 
the primary literature for the force field you've chosen for your work.  Because 
you've scrutinized the literature and know about why you've chosen that 
particular force field, right?

-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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