Smith, Micholas D. smithmd at ornl.gov
Wed Oct 8 14:28:30 CEST 2014

In addition to Justin's suggestions, I would highly recommend looking at Rapport's book: D. C. Rapaport (1996) The Art of Molecular Dynamics Simulation. ISBN 0-521-44561-2. It is a standard go-to for the foundations of MD simulations. 



Micholas D. Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
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, October 08, 2014 7:33 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] BASIC FOUNDATION/CONCEPTS used in GROMACS

On 10/8/14 7:18 AM, amitabh jayaswal wrote:
> Dear All,
> Greetings!
> 1. By education and training and experience I've been a Biologist.
> 2. I'm attempting MD Simulations for the first time in life.
> 3. Because of the neatly designed tutorials by Dr. J. Lemkul I've been able
> to do MD of/from the tutorials.
> 4. But I'm still struggling with the concepts OR the foundations which
> GROMACS uses. For example:
> a.) The mathematical terms.
> b.) The computational jargon-flags, options, parameters...
> c.) The CONCEPTS of MD SIMULATION itself - used by GROMACS; say why LJ
> potential? What relevance it has to MD? Why was it chosen over other
> alternatives?
> These I need to UNDERSTAND to be able to make any sense out of my success
> at GROMACS and do some worthwhile analysis.
> Please guide me by pointing to some suitable forum (the GROMACS fora seems
> too technically advanced for me right now) OR text.

Try textbooks by Cramer, Leach, or Frenkel and Smit.



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

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