[gmx-users] system is exploding!!!!!

Mark Abraham mark.abraham at anu.edu.au
Tue Jul 11 01:58:54 CEST 2006


Please avoid the use of multiple exclamation marks or capitals in
subjects. The problem may be of tremendous significance to you, but your
urgency means very little to the others of us, and you will get more
helpful feedback if you sound like you are describing your symptoms calmly
and clearly. :-) Fortunately the text of your email did this, but some
people might discard your message unread because of such a subject...

> I have recently upgraded to gromacs3.3. I was running
> an MD simulation of a protein-ion complex immersed in
> water, on gromacs3.2 before and it worked fine. Later
> I rerun the same simulation on gromacs 3.3 but with
> different starting velocity. I am getting this error
> now:
> Warning: 1-4 interaction between 1271 and 1277 at
> distance 2.846 which is larger than the 1-4 table size
> 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your
> mdp file
> I found online that many people are facing similar
> kind of problem but I am not sure of the solution.
> Kindly let me know.

I suggest you look carefully at the before and after configurations,
because this may tell you that your topology is broken. Re-use pdb2gmx to
generate a new topology and see where they might differ. If your
topologies are fine, which I doubt, then you should re-do energy
minimization before generating new velocities.


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