[gmx-users] Learning MD

[ms]

On 11/05/10 05:17, sonali dhindwal wrote:
> Thanks a lot for your replies. I will start reading this and learning MD.
> I really want to say that this forum is an excellent source of help.
> Thanks for all your help.

Another book you may want to read is "Understanding molecular 
simulation", by Daan Frenkel and Berend Smit. It also covers issues not 
related strictly to molecular dynamics, like MonteCarlo techniques, but 
it is a very good resource.

m.

>
> Regards
> --
> Sonali Dhindwal
>
> --- On Mon, 10/5/10, Justin A. Lemkul<jalemkul at vt.edu>  wrote:
>
> From: Justin A. Lemkul<jalemkul at vt.edu>
> Subject: Re: [gmx-users] Learning MD
> To: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
> Date: Monday, 10 May, 2010, 10:43 PM
>
>
>
> 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:
>
> http://en.wikipedia.org/wiki/Molecular_dynamics#References
>
> 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 material.
>
> -Justin
>
>> Regards
>> --
>> Sonali Dhindwal
>>
>>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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