[gmx-users] Use NVT to mimic NVE
mrshirts at gmail.com
Sun Oct 12 20:07:42 CEST 2014
> The point was that if the energy leaves the system, then the system
is never in equilibrium. Not vice versa, please.
This is incorrect logic. f there are errors in the integrator, then
F=gradient of the potential is not true. If that is not true, energy is not
conserved, and energy can leave or enter the system.
On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> The point was that if the energy leaves the system, then the system is
> never in equilibrium. Not vice versa, please.
> Dr. Vitaly V. Chaban
> Виталий Витальевич ЧАБАН
> On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> > 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
> > equilibrium.
> > I guess people use the word "converge" instead of equilibrium in
> > 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
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