I am doing a 10 ns MD simulationon a 10bp oligonucleotide on a
single pentium III 1000Mhz.
I'm encountering trouble with RMS deviation too large, cannot
reset coordinates
...
FATAL error
I understand the problem is that my molecules has a too strong
deviation so the coordinate resetting cannot be done.
But, i ran, from a previous restart file, the same calculation on
my indigo2 (R10000), and it worked fine.
Is it repeatable on the PC?
It could be a precision problem, but i didn't saw any warning
about this kind of difference between x86 architecture and SGI's
one.
Shouldn't be that..
First of all, i would like to know if the problem i encounter
could be due to the architecture.
If it's repeatable, it could be due to the architecture but in a
trivial way - trajectories diverge due to different floating point
implementations. It used to be that the only 2 architectures that
gave exactly equal results over a whole trajectory were HP & PC/g77,
so it would be interesting to see if it failed the same way on an HP.
Also it'd be interesting to diff the sgi/pc outputs & watch the
divergence.
However, if it's repeatable, I think it more likely that there is
some bug at the compiler/library level on your PC. Possibly updating
versions would help.
Is there a difference in sander_classic and the MA Young sander,
from the center mass resetting point of view.
I'm not familiar with the MA Young version.
Last point :
Is it conceivable to finish an MD simulation which began under
intel/linux (32-bit) on an indigo2/IRIX (i.e. on another platform
...)
Yes.
Bill Ross
Received on Fri Jun 22 2001 - 13:51:17 PDT
