[gmx-users] hints for core/shell optimization?

Tamas Karpati tkarpati at gmail.com
Fri Jul 25 17:22:07 CEST 2014

Dear Justin,

> Does your topology specify the proper intramolecular exclusions?  What
> is(are) the molecule(s)?

No bonds, no exclusions. The whole crystal is modelled by ions
interacting via forces of the Coulomb and Buckingham types.
In fact, there is an X-Y-X angle force type which does have an
effect on forces and energy. Shell particles, on the other hand,
are defined via the [polarization] section as quasi-bonds. That's all.

> Try nstlist = 1.  The shell positions are solved via SCF (EM), so you need
> to update the neighbor list very frequently.

Thanks for the trick. Tried but to no avail (very same results).
Although shells should have their weight in the model, I expect
them not to frequently change partner -each is ultimately connected
to its core atomic site.
In addition, there are no more bonds in the system i, thus, don't
see the point in regenerating pairs. Is there a process -I should
get to know about- which autogenerates bonds?

Thanks al lot for you help.

Best regards,

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