[gmx-users] General Questions about Molecular Dynamics

[Lara Bunte]

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?

greetings
Lara
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