From owner-chemistry -8 at 8- ccl.net Sun Jan 29 19:16:01 2006
From: "Dr. Seth Olsen s.olsen1^uq.edu.au" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: MD software question.
Message-Id: <-30690-060129184000-20832-ZJlsyfeNbMsydqnUonUZig . server.ccl.net>
X-Original-From: "Dr. Seth Olsen" <s.olsen1() uq.edu.au>
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Date: Mon, 30 Jan 2006 09:39:53 +1000
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Sent to CCL by: "Dr. Seth Olsen" [s.olsen1,+,uq.edu.au]

Even for MD packages that are not specifically designed for proteins, 
there are still complications that go beyond just solving Newton's 
equation.  Since the number of pairs for interactions scales as N**2, it 
is usually best if more complicated algorithms are used for finding 
pairs between which to evaluate different terms.  Electrostatics are 
long-range (i.e. you will want to evaluate these between many pairs), 
but vdW terms are much shorter (you don't need to many pairs - it would 
be foolish to evaluate Lennard-Jones terms between molecules 50 angstrom 
apart!).  Of course bonded terms are 'short range', but you still need 
to build pair lists.  For a good, clear & well written discussion I 
recommend Allen & Tildesley's 'Computer Simulation of Liquids'.  It's 
older, but not outdated and the writing is quite clear and smooth (a 
huge bonus for a tekkie book).

For biomolecular simulations, software packages usually have additional 
complication designed to tailor to these systems.  I just bought 
'Molecular Modeling and Simulation - an Interdisciplary Guide' and it's 
next on my reading list.  The reviews on Amazon are good for this one.  
You should also be able to find good reviews in the literature.

Many programs also have auxilliary programs to help in setting up your 
system prior to simulation (particularly if you are dealing with, for 
example, an unnatural amino acid or unparametrized ligand).  A good 
example of these are the Antechamber or Xleap modules of Amber.

For more detailed discussion, I must refer to someone more cognate than 
me.  I'm just starting getting ready for MD.  By training so far I do 
excited-state quantum chem.

Cheers,

Seth

Don Steiger sd00_2002::yahoo.com wrote:

>Sent to CCL by: "Don  Steiger" [sd00_2002[-]yahoo.com]
>I have an MD question.  As far as I can tell, the equations/math that goes into MD are fairly straight forward and short. Yet there are a lot of MD packages, and all of them are very large.  So what is in these packages that makes them so large?>
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