Re: Re: too much rattle

From: Brian Bennion (
Date: Thu Feb 12 2004 - 16:50:30 CST

Hello Amarda,

I don't mean to be incipeint but a 1000K or degrees is a bit extreme
especially if at the previous timestep the temp is 0 Kelvin. The rattle
algorithm wasn't built for those velocities. In fact a lot a minimization
is needed when solvent has been placed around a protein or ions for that
matter. Having said all that, you can turn it off if you want.


On Thu, 12 Feb 2004, Amarda Shehu wrote:

> Does anyone know how to deal with constraint failures in the RATTLE
> algorithm? I have been trying to heat up the solvent with ions for a
> protein system that is fixed, temperature set to 1000. However, I have had
> continuous problems with certain atoms shaking too much and the whole
> system becoming unstable. I thought doing some minizations to equilibrate
> the system on the fly would do the trick. However, it seems that there is
> always one atom (not the same one, varies from simulation to simulation)
> that destabilizes the system. Do I need more minizations?
> I have checked that my system is well inside the bounding box.
> Does anyone have any word of direction?
> Thank you,
> Amarda Shehu.
> Computer Science Department,
> Rice University.

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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