[gmx-users] mdp file

Sotirios Dionysios I. Papadatos si.papadatos at edu.cut.ac.cy
Fri Sep 4 12:40:10 CEST 2015

Thanks for your quick reply. Up till now all the simulations I have performed are with the OPLS force field, because the software I used in the past supported only that in the academic version. 
Anyway, to sum it up for non bonded from the literature about a particular force field and try some tutorials. Got it.
Thank you so much

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Wednesday, September 2, 2015 12:26 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] mdp file

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.


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 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

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