Subject: intro text on MD

From: Goutam Das <[email-masked]>
Date: Thu, 18 Feb 1999 23:11:20 -0600

Folks,

A very big thank you to all those of you who responded with very helpful
suggestions.  I have also received several requests for summaries  and this
appears below:

1. Hi Goutam,

  You may wish to look into the following references:

  [1] D.Frenkel and B.Smit, "Understanding Molecular Simulation -
  From algorithms to applications", Academic Press, 1996. (You can also
  try to check http://www.hpcn.tudelft.nl/frenkel_smit.html)

  [2] M.P.Allen and  D.J.Tildesley, "Computer simulation of liquids",
  Clarendon Press, Oxford, 1987 (Sometimes people call this book
  "the bible").

  [3] O.Teleman, B.Jonsson and S.Engstrom, J.Chem.Educ.70,p.641
  (1993).

  [4] http://gserv1.dl.ac.uk/CCP/CCP5/main.html

  [5] http://antas.agraria.uniss.it/

  / Fernando.
E-mail: [email-masked]             +46 (46) 2220381 (office)
        [email-masked]

         http://www.fkem2.lth.se/personnel/fernando/dasilva.html
         http://idefix.ffclrp.usp.br/barroso/fernando.html

2. Dear Goutam,

I teach a course on Kinetics and Molecular Dynamics in
the University of Girona. We use a program that it is based
on the paper by Fernadez, Sordo & Sordo J. Chem. Educ. 62 (1985) 491
to analyze the H + H2 dynamics and the response from the
students is usually quite good.

Hope this helps,

Miquel

 World Wide Web: http://iqc.udg.es/~miquel/mike.html
 e-mail: [email-masked]

3.  Sender: [email-masked]
Hello,

there is a very nice introduction into MD from Furio Ercolessi. Have a look at
his page
http://www.sissa.it/~furio/

Regards

Anselm Horn

4.  From: Jan De Kerpel <[email-masked]>

I can advise you the book of Andrew Leach called Molecular Modelling:
principles and applications, Publisher Longman Harlow, 1996 which
includes a good chapter on all kinds of MD, including theory and
applications. There are also books for special work, e.g. medicinal
chemistry, protein modeling etc...

5.  The classic book is "Computer Simulation of Liquids", by M.P. Allen and D.
J. Tildesley.  This has excellent coverage of the basic methods in MD.
Other choices include "Molecular Dynamics Simulation" by J. M. Haile and
"The Art of Molecular Dynamics Simulation" by D. C. Rapaport.  Both have
their good points, but neither is as useful as Allen & Tildesley.  I have
heard that "Understanding Molecular Simulation" by D. Frenkal and B. Smit
is good as well, but I have never seen it.

I hope these are helpful.

-Steve Stuart
Department of Chemistry
Clemson University

6.  The four texts are just about all you need to get started.  The first
two are the most elementary. Allen and Tildesley has programs on a
Microfiche which are also downloadable on line.

You may also be interested in a play with my MD simulation code (for
solids and liquids, not flexible biomolecules).  It's called Moldy and
there's a pre-compiled PC version.the web page
"http://www.earth.ox.ac.uk/~keith/moldy.html" which also has links to
other well-known simulation programs and resources.

@Book{haile:92,
  author =	 {J. M. Haile},
  title = 	 {Molecular Dynamics Simulation},
  publisher = 	 {Wiley},
  year = 	 1992,
  address =	 {New York}
}

@Book{rapaport:95,
  author =	 {D. C. Rapaport},
  title = 	 {The art of molecular dynamics simulation},
  publisher = 	 {Cambridge University Press},
  year = 	 1995,
  address =	 {CAMBRIDGE}
}

@book{allen:87,
     ADDRESS = {Oxford},
     AUTHOR = {M. P. Allen and D. J. Tildesley},
     PUBLISHER = {Clarendon Press},
     TITLE = {Computer simulation of liquids},
     YEAR =  1987
}

@Book{frenkel:96,
  author =	 {Daan Frenkel and Berend Smit},
  title = 	 {Understanding Molecular simulation},
  publisher = 	 {Academic Press},
  year = 	 1996,
  address =	 {San Diego}
}

Keith Refson
--
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Email: Keith.Refson@  | Tel: +44 1865 272026 | Dr Keith Refson,              |
       earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences        |
                                             | Parks Road, Oxford OX1 3PR, UK|
------------------------------------------------------------------------------

7.
You may be interessed by these :

1. Bruce R. Gelin, Molecular Modeling of Polymers Structures and
Properties, Hanser/Gardner Publications, 1994

2. M.P. Allen et D.J. Tildesley, Computer Simulation of Liquids, Oxford
Science Publications, 1987.

3. Elisabeth A. Colbourn, Computer Simulation of Polymers, Longman Group UK
Limited, 1994.

There is also some good texts by David Young that you can find on the Web.
They are attached to this message...

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Mathieu Roberge

Dept. Chimie, Universite Laval
Cite universitaire, Ste-Foy (Quebec) Canada, G1K 7P4
(418) 656-2131 poste 4210

2450 Place Prével, #2
Ste-Foy, Québec
G1V 2X3
(418) 650-7199

[email-masked]

I hope all these help.

Goutam Das

GOUTAM  DAS, Ph.D
BETZDEARBORN (A division of Hercules)
PO BOX 4300, 9669 GROGANS MILL ROAD
THE WOODLANDS, TX 77387-4300
# 281.367.6201 xt 425///email:[email-masked]