[gmx-users] Re: Re: gmx-users digest, Vol 1 #653 - 10 msgs

[Michael Shirts]

Actually, this might be considered more a problem with Berendsen temperature
scaling methods, which additionally simulate an ensemble that is not actually
NPT; a temperature control mechanism such as an Andersen thermostat (periodic
stochastic collisions with particles in the box with a time constant
sufficiently not to mess up the dynamics much) will not exhibit such partition
of energy into seperate modes.  I'm not sure about Nose-Hoover temperature
control methods - anybody know?

Cheers,
Michael Shirts

> Date: Tue, 04 Mar 2003 14:13:08 -0600
> To: gmx-users at gromacs.org
> From: Eric Jakobsson <jake at ncsa.uiuc.edu>
> Subject: Re: [gmx-users] Re: gmx-users digest, Vol 1 #653 - 10 msgs
> Reply-To: gmx-users at gromacs.org
>
> This is a particularly egregious problem with PME.  We published on this in
> J. Comp. Chem. a couple of years ago.  It is the "flying ice cube"
> effect--as the translational motion builds up the heat bath keeps v squared
> the same so the temperature goes down, and if you let it go you have an ice
> cube hurtling through space very fast.
>
> As Erik says, the solution is to keep resetting the center-of-mass motion
> to zero.
>
> Eric


Cheers,
Michael