Linux stability

From: Stephane <>
Date: Sat 23 Jun 2001 00:05:29 +0200

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.

It could be a precision problem, but i didn't saw any warning
about this kind of difference between x86 architecture and SGI's

First of all, i would like to know if the problem i encounter
could be due to the architecture.
If so, sould we consider buying cheap cluster of x86 (INTEL or
AMD) under linux, or 64-bit computers ?

Secondly, i must mention that my MD ran through 3.9 ns without
trouble, so isn't it possible that the resetting of center-mass
goes wrong somewhere.

To check both of that, i tried to compile the MA Young version of
sander, but cannot obtain the final sander.

So this is others points :

Is there a way to compile sander4.1, and so the MA Young version
of sander under linux (red hat 7.0). I tried to copy Machine.g77
and Machine/g77 to the amber4.1 package, but it didn't worked.

Is there a difference in sander_classic and the MA Young sander,
from the center mass resetting point of view.

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

Thanks a lot in advance.

Teletchea Stephane - CNRS UMR 8601
Lab. de chimie et biochimie pharmacologiques et toxicologiques
45 rue des Saints-Peres 75270 Paris cedex 06
tel : (33) - 1 42 86 20 86 - fax : (33) - 1 42 86 83 87
mel :
Received on Fri Jun 22 2001 - 15:05:29 PDT
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