Thanks Mark.
Are the results obtained from the ( well behaving ) simulations on A and B
platforms reliable ?
Ester
----- Original Message -----
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Wednesday, January 11, 2012 12:27 PM
Subject: Re: [gmx-users] platform dependent fate of a md simulation
On 11/01/2012 9:18 PM, Ester Chiessi wrote:
Hi,
running a md simulation with the same tpr file ( using Gromacs 4.5.3 ) on
three different platforms ( A: HP xw8600 Workstation; B: PC with Intel CORE 2
DUO processor; C: IBM Power6 cluster ), I obtained the following results:
on A and B platforms the run is fine,
on C the run crashes at the first step, returning LINCS errors.
Did anyone observe this behaviour? What does it mean?
I wonder if my system is really wrong or not.
I noted this difference in the corresponding md.log files:
Platform A RMS relative constraint deviation after constraining:
3.56e-06
Platform B RMS relative constraint deviation after constraining:
3.48e-06
Platform C RMS relative constraint deviation after constraining:
3.58e-06
Really many thanks for any comment.
See http://www.gromacs.org/Documentation/Terminology/Reproducibility for
general discussion. Probably A and B are getting lucky with the numerical
integration of a poorly conditioned system, and C is not. For advice on fixing
the problem, see http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Mark
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