[gmx-users] BASIC FOUNDATION/CONCEPTS used in GROMACS

[Justin Lemkul]

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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