[gmx-users] Some basics

Y. U. Sasidhar sasidhar at chem.iitb.ac.in
Sun Jun 15 16:56:02 CEST 2003

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
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try the book by Andrew Leach "Molecular modelling"

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


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