[gmx-users] General Questions about Molecular Dynamics

[Jussi Lehtola]

On Sun, 25 Dec 2011 20:45:44 +0000 (GMT)
Lara Bunte <lara.bunte at yahoo.de> wrote:
> Hello
> 
> I have a few questions about molecular dynamics simulations.
> 
> 1) For a molecule Newton's equation of motion is solved. Do I get
> here one resulting force for the hole molecule or do I get a lot of
> forces, one for each atom?

YMMV. If you're using an united atom force field, e.g. the methyl
groups (CH3) will be represented as a single fictitious atom. If, on
the other hand you're using an all-atom force field every atom will be
present explicitly in the calculation and you will get forces for every
one of them.

Some force fields even have more fictitious particles than physical
atoms; e.g. the tip4p force field for water is a four-site model that
includes a dummy atom.

> 2) The force is calculated from the potential. This consists of the
> sum of potentials linear vibration, oscillation angle, torsional and
> non-binding parts as Coulomb and Lennard-Jones potential.
> 
> How do you calculate the parameters for these potentials? I heard
> something about QM calculations but what do they how calculate?

You can obtain parameters either directly from experiment (may be
nontrivial) or from high-level QM calculations, or indirectly by
fitting the parameters in order to reproduce the experimental values
for quantities such as particle densities and radial distribution
functions.

In QM calculations one basically solves the Schrödinger (or
Dirac) equation that describes the behavior of electrons, which are
responsible for practically all of the properties of "normal" matter.
You can find more by googling about quantum chemistry.

The construction of force fields is, however, somewhat of a black art.
It is perfectly possible to construct a seemingly sensible force field
that ends up giving bad results.
-- 
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Mr. Jussi Lehtola, M. Sc.         Doctoral Student
jussi.lehtola at helsinki.fi         Department of Physics
http://www.helsinki.fi/~jzlehtol  University of Helsinki
Office phone: +358 9 191 50 632   Finland
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Jussi Lehtola, FM                 Tohtorikoulutettava
jussi.lehtola at helsinki.fi         Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632
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