From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Wed Jul 18 2007 - 15:36:37 CDT
Josh,
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.
Regards,
Dave
On Jul 18, 2007, at 1:02 PM, jadelman_at_berkeley.edu 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
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/
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