[gmx-users] Some basics

Peter C. Lai sirmoo at cowbert.2y.net
Sun Jun 15 21:38:01 CEST 2003

Much of the theory is tied into statistical mechanics and thermodynamics
A textbook which explains ensembles, algorithms, and coupling in the context 
of MD is:

D. Frenkel and B. Smit, Understanding Molecular Simulation
 From Algorithms to Applications, 2nd Ed.
Academic Press 2001

On Sun, Jun 15, 2003 at 07:18:45PM +0530, 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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Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology
Yale University School of Medicine
SenseLab | Research Assistant

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