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

Pedro Alexandre de Araújo Gomes Lapido Loureiro palaplou at gmail.com
Tue Mar 13 22:01:33 CET 2007

> Pedro: I've already expanded the box increadibly much (say, 200
> angstrons in each direction), and the problem still remains. I mean,
> expanded it from an original box with size to fit the experimental
> density.

Yes, but if the problem is higher-than-experimental density, then expanding
the box will not solve it, because the molecules will try to reduce
instantly the density. That's just what you don't want.
Besides, expanding the box will reduce it only after equilibrium has been

> Low temperatures where already tested in the C9 but not in the C8,
> I'll try later. I've tried 98.15K for 200ps, but at the moment I don't
> quite remember if it blowed at that temperature or when I tried to
> increase it.

I was suggesting even lower temperatures.

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