Subject: Molecular Dynamics answers

From: JEREMY WALTON <[email-masked]>
Date: 23 Nov 93 13:11:00 WET

Hi Noy,

>>        1) Is it possible to apply a "scaling temperature" algorithm
>>to control the temperature range ( my MD is NVE ) ? To my idea,
>>scaling the velocities cause the deviation of the p-q coordinate
>>( generalized momentum-generalized coordinates ) in the phase space.
>>The trajectories are therefore deviated, is it true ? How to scale
>>both velocities and coordinates to keep the correct trajectories and
>>p-q coordinates in the phase space ?

The traditional way to get the NVE simulation running at (close to) the 
temperature you want is to have an equilibration period where the velocities
are all uniformly scaled so the system is forced to have the kinetic energy
appropriate to the required temperature.  Following this period (typically
a few thousand timesteps), scaling is switched off and the averaging over
configurations can be started.  The temperature should be monitored during this
averaging period (it's one of the things you calculate as an average); if it
drifts too much, then maybe the equilibration period wasn't long enough, or
maybe your timestep is too big.

>>        2) Is it possible to apply an "external bath" in which is
>>generally used with NVT ensemble to an NVE ensemble ?

There are a number of algorithms for this.  Two which I recall are that of 
Berendsen and that of Nose.  Check out Allen & Tildesley's "Computer Simulation
of Liquids" (OUP, 1987), where all this is described in some detail.

Hope this helps,

Jeremy

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