CCL: MD software question.

 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 It's older, but not outdated and the writing is quite clear and smooth (a huge bonus for a tekkie book).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?>