CCL: MD software question.

James already pointed out some indications for the very many number of
MD programs around; but I think the major issue is the F in the F=ma
equation, i.e. the force field. It is very difficult to construct a
force field that is equally valid for all different kinds of systems
that MD simulations are used on.

For instance, there have been force fields suited for MD simulations
of organic solutes (OPLS), or biosystems (AMBER, GROMOS, CHARMM), but
also that are mainly for geometry optimizations of organic molecules
(MM2, Dreiding, MMFF94), and many many more ..
Please note that this is just my short-cut summary of the many force fields around,
so don't be offended if your favorite FF is not listed on it..

Of course, in the end, the best programs are those that allow to choose between
any of the most relevant ones without any problems..

On Sunday, January 29, 2006, at 08:10 PM, JAMES VIVIAN jamestvivian()msn.com wrote:

Don:
You're basically correct that at the conceptual & mathematical level, things
are pretty straightforward; you need to create & store ~3*N coordinates for
N particles, and F=ma tells the story. So you then need an integrator. And
a force-field. And maybe a linked-list (Verlet), and some trickerly for
periodic-boundary conditions, etc.. But the core or heart of the MD
simulation remains a fairly brief chunk of code, much like the engine in a
car is a relatively small fraction of the whole beast.

Once you factor in the GUI, the flexibility to elect different ensembles
(NVT, NPT, uVT Grand Canonical...), different force field / energetic
options, solvation, build in constraints, SHAKE, RATTLE, thermostats, etc.,
then things tend to spawn. So to craft a generally multi-purpose MD
package, things tend to get unwieldly in a hurry. And a lot of packages
don't just stop at generating trajectories; they'll allow you to do some
degree of post-processing, maybe even allow you to evaluate a time
correlation function, etc..

So they end up being non-trivial and worth the $$$ when you assemble all the
pieces in a shrink-wrapped package.
––––––––––––––––––––––––––––––––––––––––––––
dr. Marcel Swart

Theoretische Chemie (kamer R152)
Vrije Universiteit Amsterdam
Faculteit der Exacte Wetenschappen

De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

T +31-(0)20-5987619
F +31-(0)20-5987629
E m.swart ~~ few.vu.nl
W http://www.few.vu.nl/~swart
––––––––––––––––––––––––––––––––––––––––––––
Starting May 1, 2006:

ICREA researcher at
Institut de Química Computacional
Universitat de Girona

Campus Montilivi
17071 Girona
Catalunya (Spain)
––––––––––––––––––––––––––––––––––––––––––––