[gmx-developers] (no subject)

[Erik Lindahl]

Hi,

Great oliver - thanks!

Cheers,

Erik

On Jan 31, 2006, at 3:48 PM, Oliver Lange wrote:

> Hi,
>
> thank you for the bug-report.
> This bug is new. It did not exist in Gromacs 3.2.1.
> As a work-around, just remove the offending line as long as you  
> don't use edsampling
> ** bHaveConstr = bHaveConstr || ed_constraints(edyn);  **
>
> The problem exists, because edsam is not really implemented with  
> parallelism in mind. Thus, the slaves do not no if edsampling is  
> switched on or not.
> I will implement a MPI -communication step to amend this in the  
> initialization step, and upload this to CVS.
>
> Oliver
>
> H.J.Risselada wrote:
>
>>
>> Dear gmx-developers,
>>
>> I discovered a bug in GROMACS-3.3 in mdlib/update.c concerning the  
>> usage of constraints.
>>
>> I discovered that the temperature on the slaves during a parallel  
>> run was 30 K lower at ref_t 300 K then on the master at all times.
>>
>> I used a LJ-particles only test system without constaints:
>>
>> Constaints where put on "none" in the mdp file.
>>
>> However,
>>
>>  /* if edyn->bEdsam == FALSE --- this has no effect */
>>     bHaveConstr = bHaveConstr || ed_constraints(edyn);
>>
>> returns FALSE on the master, but TRUE on the slaves.
>>
>> This means that the constrainst loops become active on the slaves,  
>> which will interfere with the dynamics.
>>
>> When T-coupling is used, one temperature group can be both devided  
>> on the master as on the slaves. The total mean temperature of the  
>> T-group will be the desired temperature.
>> However the desired maxwell distribution will be disrupted.
>>
>> This Bug may have a significant effect on the users of GC-models.
>>
>> I tested it for the version 3.3, but it may also be present in the  
>> older versions.
>>
>> greetings
>>
>> Jelger.
>>
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>>
>>
>
> -- 
> Oliver Lange
> MPI for biophysical Chemistry
> olange at gwdg.de
> Fax: +495512012302
> Tel: +495512012305
>
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-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214