[gmx-users] What becomes of kinetic energy in local minima?
Mark.Abraham at anu.edu.au
Thu May 14 02:39:10 CEST 2009
yutong.zhao at utoronto.ca wrote:
> Hi Gmx,
> I often hear the notion that "simulations" get stuck in local minima
> (for potential energy I assume), how come? What happens to the "kinetic
> energy" that is supposed to kick the system out of local minima? (ie.
> when I roll a marble down a dip it tends to come out so long as there's
> no friction. If the barrier is too high then wouldn't the system would
> sort of "oscillate" in the well?
Yes, that's exactly what can happen. Dynamical simulations can get
trapped in a well if its depth is a suitable multiple of kT.
> How does GMX treat KE loss via
> micromolecular friction?
There isn't any. MDS integrate Newton's laws. Under constant-energy
conditions (NVE), energy can only convert from form to form. Under
constant-temperature conditions (NVT, NPT), velocities are manipulated
to keep the average T near a value.
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