[gmx-users] Triggering generic kernel causes LINCS warnings

Pieter van 't Hof pvanthof at xs4all.nl
Tue Jan 12 13:26:22 CET 2010

Hi Berk,

Thanks for your quick answer. Are the modifications done only in
nb_generic.c, so I could 'patch' my altered version of 4.0.5?


> Hi,
> This is a bug which I fixed in 4.0.7 (but somehow it is missing from the
> revision list).
> Berk
>> Date: Tue, 12 Jan 2010 12:11:23 +0100
>> From: pvanthof at xs4all.nl
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] Triggering generic kernel causes LINCS warnings
>> Hello,
>> I'm trying to simulate a water box with protein and drug. Having set up
>> the simulation, starting mdrun causes no problems on its own. However,
>> after setting the GMX_NB_GENERIC environment variable and restarting the
>> simulation, it crashes at step 20 with too many LINCS warnings.
>> Disabeling
>> the environment variable makes mdrun run normal again.
>> Where is this different behavior coming from and is this solvable?
>> Using Gromacs 4.0.5. Attached the screen output and the log file.
>> Thanks in advance,
>> Pieter van 't Hof
>> Graduate student Utrecht University
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