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

[Mark Abraham]

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:Mark.Abraham at anu.edu.au>
>     *To:* Discussion list for GROMACS users
>     <mailto:gmx-users at gromacs.org>
>     *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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