[gmx-users] system reshaped on itanium II

Jens Krüger mercutio at uni-paderborn.de
Thu Mar 3 18:04:17 CET 2005


I observed a strange behavior of my simulation systems on a new Itanium
II Cluster. Whatever system I use, it behaves well on a normal P4, but
when transferred to the Cluster, the box expands along the z-axis and
the water molecules "regroup" from typical brick shape to an
octahedral-bipyramidal shape. After ca. 50 ps the whole system crashes.
I varied all parameters and rebuilt the systems from scratch but the
problem still remains.

What I have tried so far:
- changed the number of nodes
- varied pcoupltype (none, isotropic, ...) with different coupling
- varied Tcoupl
- varied coulombtype (cut-off and PME) with different parameters
- tried all variations of grompp with or without -shuffle -sort
- double checked, if I am really using a cubic/tric system and NOT a
- used clean protein/water, DPPC/water and protein/POPE/water, each
running stable on a Linux  P4
- energy minimization cg and steep

All of them did not had any influence on that strange failure.

Has anybody an idea what might by the reason?


Jens Krueger
mercutio at uni-paderborn.de
Warburger Str. 100 * 33098 Paderborn * Tel.:05251-602183
Warburger Str. 64 * 33098 Paderborn * Tel.:05251-2025608

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