[gmx-users] Large Molecule Stability

Evan Lowry evanwlowry at gmail.com
Sun Sep 11 19:19:18 CEST 2016

Dear Gromacs Users,

I am working with a very large molecule that has 580 atoms and am trying to
conduct NVT simulations. Unfortunately, GROMACS is highly unstable with
this molecule and keeps crashing even with LINCS and a time step of 0.1 fs.
I have checked and rechecked the structure but keep getting the following

WARNING: nonbonded interaction between particles... is larger than the
table limit...

Is this due to the size of the molecule (+3nm long) or charge groups? I am
out of simulation options to change and was hoping someone may have some
suggestions for increasing the stability of the simulation.

I would welcome any suggestions.


Evan L.

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