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

[amitabh jayaswal]

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.
Best regards.

Amitabh Jayaswal
Research Scholar, Bioinformatics
Mahila Mahavidyalaya, MMV
Banaras Hindu University, BHU
Varanasi, Uttar Pradesh, India. PIN-221 005
MOBILE PHONEs: +91 9868 330088,
                             +91 7376 019155