AMBER Archive (2008)

Subject: Re: AMBER: Re: timestep problem

From: David A. Case (
Date: Thu Jan 17 2008 - 14:27:56 CST

On Thu, Jan 17, 2008, Andrey Semichaevsky wrote:
> I am running a "sample preparation" simulation of an RNA molecule in the
> water solution with the sodium and chlorine ions, using PMEMD in Amber 9.
> The timestep necessary for the stability of the heating procedure seems to
> strongly depend on the sodium ion concentration that are added in excess of
> the sodium concentration that is necessary to neutralize the phosphate
> groups in the molecule. To make the simulation run without any exceedances
> of the velocity limit (vlimit), I have to decrease the timestep dt
> approximately 2-fold compared to the simulation of the same system but
> without the excess ions. Could you suggest what the source of the problem
> could be. Thanks.

Occasional vlimit violations are not a problem, especially during
equilibration. Unless you are getting many of these, or lots of them persist
after the temperature has settled down, I would not worry about it.


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