[gmx-users] Some basics

[Y. U. Sasidhar]

Aswin Narain wrote:

> Dear gmx -users,
> I have, so far sent a few mails to the group. I am a newbie to gromacs 
> and am learning it by practice. Now I have come to a situation in 
> which I need to know a bit of theory as well. I want to know about the 
> different algorithms that are being used in gromacs. I just know the 
> names, as I saw in the manual. But then I should know what these 
> algorithms actually do, in simple terms. I also want to know about 
> constraints. What exactly are they and how do I use them in my 
> simulations? I also would like to know the basics of temperature and 
> pressure coupling. The material given in the manual goes really over 
> my head.
> If sombody could direct me to resources on these topics, I will be 
> very grateful.
>
> Thanx
>
> Aswin
>
> _________________________________________________________________
> Attention NRIs! Send money home in a jiffy. 
> http://server1.msn.co.in/msnleads/citibankrca/citibankrca2.asp
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
>
try the book by Andrew Leach "Molecular modelling"
Also:
http://diamond.kist.re.kr/SMS/papers/Ercolessi%20-%20MD%20Primer.pdf
http://www.fisica.uniud.it/~ercolessi/md/md/

there is also an excellent review article :
W.F. van Gunsteren and H.J.C. Berendsen
Computer Simulation of Molecular Dynamics: Methodology, Applications and
Perspectives in Chemistry
Angew. Chem. Int. Ed. Engl. *29* (1990) 992-1023


-- 
 Sasidhar