[gmx-users] compiler options

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 10 13:45:01 CEST 2003

On Thu, 2003-10-09 at 20:03, Shrivastava, Indira (NIH/NCI) wrote:
>  Hi Gromacs users,
>  I am doing some benchmarking for a dual processor xeon cluster. 
>  I ran a 500 ps simulation on two xeons, with identical configuration 
>  and compiled gromacs software, but I got different trajectories (as 
> seen in the rmsd's of the carbon alpha atoms from the two trajectories).
>  There was a difference of ~0.05 angstroms in the rmsd's at each time step. 
> Can someone tell me why there is this difference in the trajectories? 
Do you mean there is a difference between two identical runs (i.e.
started with the same tpr file) or is there a difference between single
processor and multiprocessor? The latter is normal due to numerical
roundoff accumulating.

>  thanks
>  Indira  
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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