Re: membrane simulation ERROR rattle algorithm

From: Ajasja Ljubetič (
Date: Wed Jul 06 2011 - 06:37:10 CDT


Thanks - so the atoms do not look strange - nor on top of each other.

Are they near the periodic boundary?

> If I run the whole system without any constraints on headgroups,
> water, or protein it is not a problem and I can run with 2 fs - I find
> this a little bit strange
> Hmm, did you check the positions of the head groups in the file you are
using for the constraints?

> Should I run longer(more minimization?) or should other things be test
> before this?
Well, I'd just equlibrate for a ns or so with the on fs step (while
gradually releasing the constraints with *constraintScaling*). After
equilibration you can switch to a 2 fs step.


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