[gmx-developers] SHAKE / LINCS crash
"Pablo García Risueño"
Risueno at physik.hu-berlin.de
Fri Jan 30 11:59:09 CET 2015
> On 2015-01-29 08:43, David van der Spoel wrote:
>> On 2015-01-28 18:13, "Pablo García Risueño" wrote:
>>>
>>>> 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.
>>>
>>
>> Both shake and lincs only correct bond lengths along the direction of
>> the original bond. However, if due to an unphysical situation, e.g.
>> large forces or too long time steps, the bond rotates too much, let us
>> say 90 degrees, the problem becomes unsolvable. Mathematically that
>> could correspond to a singularity in the equations, but the equations
>> become unstable due to other problems as Mark indicated.
> There is one, unimportant, regime where LINCS (not SHAKE) will fail.
> LINCS has the restriction that the eigenvalues of the constraint
> coupling matrix should be smaller than 1, otherwise the expansion
> doesn't converge (see the P-LINCS paper). For normal simulations where
> only bonds are constrained all eigenvalues are smaller than 1. But when
> you would additionally constrain all angles in a medium or large
> molecules, eigenvalues larger than 1 will appear. However, constraining
> all angles in larger molecules is not very useful.
>
> Cheers,
>
> Berk
>>
Dear prof. Hess
Thank you very much for your reply. We had a conversation in Sept 2011 in
Zaragoza, where you told me about some errors both in SHAKE and LINCS that
happened specially for large systems after many simulation time steps.
After the explanations of prof. van der Spoel and prof. Feenstra, I find
myself a bit confused, so if you don't mind, I would like to ask you for
further clarification.
I understand the problem of "nearly orthogonality of bonds" pointed by
prof. van der Spoel. However, prof. Feenstra told me that when his
simulation crashes, he solves it by restarting the simulation in the
latest non-crashed step and increasing the number of figures of the atomic
positions. If this can solve the problem, I guess that it cannot be due to
orthogonality of bonds, but rather to constraint matrix singularity (I
expect the constraint matrix to be somewhat chaotic, so the increase of
the number of figures could solve the nearly-singularity). However, I am
not sure on what is actually the origin of the SHAKE and LINCS errors that
you told me about in the past. May you explain me a bit more on it?
Thank you very much. Best regards.
>>> 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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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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