AMBER Archive (2007)

Subject: Re: AMBER: reproducibility between software

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Mar 02 2007 - 10:43:04 CST

I very much doubt you could get the same trajectory.
Even with the same program, you only match results for
a few hundred sets if you change # cpus, etc.
Amber and NAMD are "mostly" the same but the algorithms
do differ. You should check that the initial energies are the
same, and hopefully stay the same for at least a few steps.

On 3/2/07, Stern, Julie <jvstern_at_bnl.gov> wrote:
>
> Hello,
> 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?
>
> Any comments or pointers would be helpful.
>
> Thanks.
>
> --Julie
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