TMD: different behaviour between serial and mpi versions

From: Thomas Gaillard (
Date: Tue Jun 05 2007 - 09:57:20 CDT

Targeted Molecular Dynamics works well in serial versions of NAMD, with
a nice linear decrease of the RMSD.

With exactly the same parameters, the evolution of the RMSD is totally
different with a mpi version of NAMD. The current RMSD is not able to
follow the target RMSD and the simulation eventually stops with errors
(Bad Global Exclusion Count).

This observation has been made on different architectures (x86_64 and
ibm aix), with different TMD force constants, and either in vacuo or
with PBC.

It seems that the TMD implementation with MPI is buggy.

How is it possible that the evolution of the current RMSD is different
between serial and mpi NAMD ?

I am available for more informations or tests that you could suggest.

Thomas Gaillard
Laboratoire de Biophysicochimie Moléculaire
Institut de Chimie LC3 - UMR 7177
Université Louis Pasteur
4 rue Blaise Pascal
F-67000 Strasbourg
phone: +33 (0)390 241 493
fax: +33 (0)390 241 490

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