On 11/01/2012 11:09 PM, Ester Chiessi wrote:
Thanks Mark.
Are the results obtained from the ( well behaving ) simulations on A
and B platforms reliable ?
Only after they have equilibrated, and on the evidence of the system
blowing up on C, they didn't start very close to equilibrium.
Mark
Ester
----- Original Message -----
*From:* Mark Abraham <mailto:[email protected]>
*To:* Discussion list for GROMACS users
<mailto:[email protected]>
*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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