Re: AMBER: reproducibility between software

From: Thomas Cheatham III <>
Date: Fri, 2 Mar 2007 10:32:35 -0700 (Mountain Standard Time)

> Have there been any studies or comparisons done regarding reproducibility of
> an MD result in amber vs. namd? If all the paramter options are set the same and
> the initial conditions are the same, are the algorithms in amber and namd implemented
> the same so that an exact trajectory would come out the same?

Even with the same input options, usually the communications are
non-deterministic such that you will get a different trajectory from the
same code running in parallel... A nice discussion of how the MD
trajectories are chaotic is Braxenthaler et al. Protein 29, 417 (1997).

I do know of one comparison paper comparing AMBER and NAMD on DNA
simulation (concluding roughly that the results were similar), see:
Jha et al. J. Comp. Chem. 26,1617 (2005).

Note that getting AMBER and NAMD to produce the same energetics/forces is
tricky due to differents in the default runtime parameters and as pointed
out previously, different 1-4 scaling factors (default), etc.
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Received on Sun Mar 04 2007 - 06:07:56 PST
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