Re: reproduciblity between software

From: Cesar Luis Avila (
Date: Fri Mar 02 2007 - 15:07:02 CST

For sure, from the same initial structure you won't obtain the same
trajectory. This is true even within the same program, i.e. you can
obtain different trajectories picking different ramdom seeds. It is
expected though that the general behavior of the system will be the same
for namd (charmm ff), gromacs or amber. One excellent book you can
consult is Marcel Decker's Computational Biochemistry and Biophysics. On
chapter two you can find a comparison between this different force fields.

Stern, Julie escribió:
> Hello,
> Have there been any studies or comparisons done regarding reproducibility of
> an MD result in amber vs. namd? If all the parameter 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? Where do you suppose
> the differences would be?
> Any comments or pointers would be helpful.
> Thanks.
> --Julie

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