[gmx-users] Learning MD

[Erik Marklund]

ms skrev:
> 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.
I second that. It's a very good book. Another one, the one that once 
introduced me to MD, is 'Computational Chemistry' by Guy H. Grant and W. 
Graham Richards (Oxford University Press). It's less than 100 pages and 
gives a good introduction to both MD and QM.

Erik
>
>>
>> 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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>>
>>
>>
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/