[gmx-users] Some basics

[Erik Lindahl]

I'd like to second the Frenkel & Smit recommendation; the second 
edition also fixed almost all minor typos and things. It is both 
reasonably up to date and complete.

If you'd really like to get into the details of the statistical 
mechanics theory (ensembles, constraints as a modified hamiltonian, 
etc) the book "Computer simulation of Liquids" by Allen & Tildesley is 
wonderful. Don't be fooled by the seemingly simple introduction - 
chapter 2 took me three weeks to fully understand the first time I read 
it :-)

Cheers,

Erik

On Sunday, June 15, 2003, at 12:37  PM, Peter C. Lai wrote:

> Much of the theory is tied into statistical mechanics and 
> thermodynamics
> modelling.
> 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
> http://cowbert.2y.net/
>
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