[gmx-users] NVE simulations

David L. Bostick dbostick at physics.unc.edu
Tue Jul 9 15:32:43 CEST 2002

Hello all,

When I was stating that "it all depends on the initial configuration" for
and  NVE simulation, I did not mean to imply that the equilibrium set of
configurations should depend on the initial one.  Rather, that the strange
behavior of the temperature at the beginning of the run depends on the
initial configuration.  A little finesse at the beginning of the run is
usually required to get the system to equilibrium,.. however unrealistic
the finesse is .. physically speaking.

I understand that Sid is going for the largest timestep possible as Anton
has published.  I would still recommend starting with a small timestep
until equilibrium is reached.  It really shouldn't take long to do since it
seems to be a simple, perhaps small system.  It should then be easier to
take the final configuration from the equilibrium ensemble as an initial
configuration for the simulations with a larger timestep...  Anyway, it
will give a baseline for comparison.  .. but I'm no expert.


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick

On Tue, 9 Jul 2002, Mehmet Suezen wrote:

> "David L. Bostick" wrote:
> > It all depends on that initial configuration and velocities for an NVE
> > simulation.
> Hi David,
> Isn't true that, "in principle" equilibrium configuration should not
> depend
> on initial conditions?  If not than I'd say the system is not in
> equilibrium state
> and instead of changing ensemble will extent NVT  simulation or decrease
> the integration time step before NVE run. One measure for an equlibrium
> state  would be checking Maxwell-Boltmann velocity distribution or
> Boltmann H-function where it decays to a constant value if system
> approach to equilibrium.
> Cheers,
> Mehmet

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