[email protected] 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.
Mark
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