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

Pedro Alexandre de Araújo Gomes Lapido Loureiro palaplou at gmail.com
Tue Mar 13 20:27:22 CET 2007

Hi Jones,

Another option is to begin the simulation at very low temperatures and
increasing it at, say, every 500 ps.
But it seems that your starting configuration has some problem, maybe too
high a density?
Comparing with the experimental value, how is your density?



2007/3/13, Jones de Andrade <johannesrs at gmail.com>:
> 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,
> Jones
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