[gmx-users] General Questions about Molecular Dynamics

[Justin A. Lemkul]

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?
> 

Forces per atom at each timestep can be written to the trajectory (.trr file, if 
specified with nstfout != 0), but such information is not often used.

> 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?
> 

All relevant equations are given in the manual.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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