[gmx-developers] SHAKE / LINCS crash

"Pablo García Risueño" Risueno at physik.hu-berlin.de
Wed Jan 28 18:13:31 CET 2015

> On Tue, Jan 27, 2015 at 11:26 AM, "Pablo García Risueño" <
> Risueno at physik.hu-berlin.de> wrote:
>> Dear Gromacs developers
>> My name is Pablo G. Risueño, I am a postdoc researcher at the Humboldt
>> University of Berlin. I am currently working with some colleagues in the
>> development of new constrained MD schemes.
>> A few years ago I had a conversation with prof. B. Hess, where he told
>> me
>> that both SHAKE and LINCS can make a MD simulation to crash (specially
>> for
>> large systems with many time steps). We would like to analyse the
>> problem,
>> so we would like to have some example(s) of simulation where such crash
>> happens. We would need the Gromacs input file, and the
>> coordinates/velocities files at the step before the crashing. May
>> anybody
>> help us?
> Hi,
> This is one of the easier problems in molecular dynamics. :-) You can
> probably take anybody's MD tutorial, multiply the time step by 10 and
> observe the simulation blow up from numerical instability. The constraint
> algorithm is often the first thing to fail, but it is not itself the
> problem. It seems to me that 99+% of the time the user has not prepared
> the
> system or model physics well enough, and most of the rest of the cases are
> code bugs.
> It is not clear to me that even if a constraint algorithm could be
> designed
> to satisfy such cases (of poor user input), that having it would be a good
> thing. It is irritating to have a simulation blow up because you were too
> rough with it, but it could well be worse to have your simulation succeed
> with only subtle evidence of the original problem.
> Cheers,
> Mark

Dear Mark

Thank you very much for your reply. However, if I understand it correctly,
the crash of SHAKE I am speaking about is not a consequence of poor
definition of the input, but of nearly-singularity in the constraint
system of equations to solve. I guess that the (statistical) fails in
LINCS may be due to the fact that the correction that LINCS does may not
suffice to satisfy the constraints for some given configurations.

Best regards.

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Beste Grüße.


Dr. Pablo García Risueño

Institut für Physik und IRIS Adlershof, Humboldt Universität zu Berlin,
Zum Großen Windkanal 6, 12489 Berlin, Germany

Tel. +49 030 209366369

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