[gmx-users] Learning MD

Justin A. Lemkul jalemkul at vt.edu
Mon May 10 19:13:17 CEST 2010

sonali dhindwal wrote:
> Hello All,
> I am new at MD, and i have started doing it few months ago only. I tried 
> to run some simulations but taking all the parameters using some 
> tutorials given online and have not got very good results.
> Can someone please help in suggesting what is the best way to learn MD 
> using Gromacs in terms of manuals and literature, what should be 
> referred to do a start ?
> I am sorry in advance if this query irritates someone, but any kind of 
> help will be highly appreciable.

The Gromacs manual is a fantastic resource, particularly the introductory chapters.

Beyond that, have you tried Google?  There are a number of great 
introductory-type pages that discuss some of the more basic aspects of MD.  You 
might also find some help here:


I can attest to several of the books listed there (Allen & Tildesley, Leach, and 
Schlick) being particularly useful.  Beyond that, hopefully a supervisor or 
colleagues will have some expertise and can recommend the requisite reading 


> Regards
> --
> Sonali Dhindwal


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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