[gmx-users] c6,c12 versus sigma,epsilon

[Thad Harroun]

If I'm reading the manual correctly, in section 5.6.1 on topology file
formats, the combination rule parameter under the [defaults] section means
that I can use either C6-C12 _or_ sigma-epsilon in the [nonbond-params]
(for LJ) section.

However, everything else being equal, when I run a md on what I know to be
a pre-equilibrated lipid bilayer, it crashes very early (10-20 steps)  if
I use sigma-epsilon and combination rule 3, but runs very well with c6-c12
and combination rule 1. Why? The values are equivalent and converted from
each other.

The md params are Berendsen temp and pressure coupling, and SHAKE. It
might be a clue in that every crash occurs when a spc water cannot be
settled due to a bad contact.

Thad Harroun
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tharroun at vet.ed.ac.uk