[gmx-users] platform dependent fate of a md simulation

Ester Chiessi ester.chiessi at uniroma2.it
Wed Jan 11 13:09:50 CET 2012

Thanks Mark.
Are the results obtained from the ( well behaving ) simulations on A and B platforms reliable ?

  ----- 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: 

    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



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