[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
> Attention NRIs! Send money home in a jiffy.
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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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