Re: NAMD vs. CHARMM. Is complete correspondence possible?

From: Axel Kohlmeyer (
Date: Tue Sep 09 2008 - 15:56:52 CDT

On Tue, 9 Sep 2008, Niels Johan Christensen wrote:

NJC> Dear NAMD community.

dear niels,

NJC> I have seen a fair deal of questions on NAMD-l pertaining to
NJC> differences between various output/input files used by the NAMD and
NJC> CHARMm programs.

NJC> However, I have the following pragmatic (and possibly na´ve) question:

NJC> Is it possible to carry out a simulation in NAMD using exactly the
NJC> same parameters (Same force field, equivalent configuration file
NJC> settings, etc.) as in the CHARMM program - and if that is possible,
NJC> can one rest assured that the trajectory and energies recorded in
NJC> NAMD will be comparable to those recorded in CHARMM?

they should, but it depends a lot on what you consider equivalent
or comparable. since floating point numbers are not associative
(i.e. (a+b)+c != a+(b+c)) there will always be (small) differences
depending on parallelization and the number of processors used.
within the error margins of floating point math, you should get
the same energies and forces, but that would require identical
methods for cutoffs, long-range interactions (ewald/PME) and so
on. however, due to (exponential) propagation of the differences,
trajectories from the same starting point will soon diverge, yet
sample the same statistical mechanical ensemble. in other words,
ensemble averages should be the same within statistical errors.
NJC> This question probably amounts to asking, if the various
NJC> interaction terms are (or can be) evaluated in exactly the same way

i would not call it exact but a very, very close approximation.


NJC> Best,
NJC> Niels

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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