[gmx-users] Use NVT to mimic NVE

[Johnny Lu]

Why non-equilibrium can cause lost of total energy in NVE simulation?
(baring the case that the non-equilibrium causes very large values that
causes over flow / getting out of the stable range of algorithms of
gromacs).

A closed system should have constant energy, regardless of whether it is at
equilibrium.

I guess people use the word "converge" instead of equilibrium in molecular
dynamics simulation of protein, possibly because the simulation may never
reach equilibrium with current computing power.
http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b

I may try older version of gromacs and/or not using constraint, after
checking the bug list and performance. I had never thought about that route.