Re: Extended System Conservation

From: David Hardy (
Date: Wed Jul 18 2007 - 15:36:37 CDT


NAMD's integration methods for NVT and NPT simulation use Langevin
dynamics, which introduces a friction term and a stochastic term.
The resulting system of equations no longer has a conserved "extended
energy" quantity in the way that extended Hamiltonian methods, such
as Nose-Hoover, do. However, the advantages of Langevin include
improved stability and better parallel scalability.

My understanding is that TOTAL, TOTAL2, and TOTAL3 are still
providing PE plus some averaging of KE.


On Jul 18, 2007, at 1:02 PM, wrote:

> Searching through the NAMD documentation and the mailing list, I've
> been
> unable to find where I would look to make sure that energy
> conservation is
> being enforced in the extended system when using either a thermo- or
> barostat for NVT or NPT simulations. My understanding is that TOTAL,
> TOTAL2 and TOTAL3 are only telling you about the sum of the PE and
> KE for
> the direct system.
> Thanks,
> Josh

David J. Hardy, PhD
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois

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