[gmx-developers] SHAKE / LINCS crash

Mark Abraham mark.j.abraham at gmail.com
Wed Jan 28 15:11:25 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?


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.


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