[gmx-users] Problems in C8 and C9 chains equilibration

Jones de Andrade johannesrs at gmail.com
Tue Mar 13 20:12:28 CET 2007

Hi everybody.

I would like to ask one question, basically about equilibration of
long and flexible alkyl chains.

I'm having terrible problems in equilibrating C8 and C9 chains. I've
already expanded a lot the box size, but I always fall into
segmentation faults. Also tried smaller time steps (my "standard" is
2fs), doesn't work. Reduction of the rcoulomb, rvdw and similar yields
some more steps, but also terrible slower simulations (too much of the
electrostatic calculations falling into the reciprocal part).

Moreover, in the minimization step, I've tried all the algorithms
available for minimization. None of them yields real success.

Did anybody successfully equilibrated systems like those, or similar
ones like n-octanol? Could anyone please give me some advice on this,
any extra "trick" I forgot or don't know to try to make these
molecules run?

Thanks a lot in advance for any help!

Sincerally yours,


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