AMBER Archive (2008)

Subject: AMBER: Re: timestep problem

From: Andrey Semichaevsky (
Date: Thu Jan 17 2008 - 12:24:00 CST

Hi all,
 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.
 Andrey Semichaevsky
 Postdoctoral Research Associate,
 Materials Science and Engineering,
 North Carolina State University,
 Raleigh NC
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