[gmx-users] General Questions about Molecular Dynamics

[Mark Abraham]

On 12/26/2011 7:45 AM, Lara Bunte 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?
>
> 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?

The process by which each force field is parameterized differs, and is 
best learned about by reading the original literature. References may be 
found in the GROMACS manual.

Mark

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