AMBER Archive (2005)

Subject: Re: AMBER: GB with Langevin dynamics problem 2

From: David A. Case (case_at_scripps.edu)
Date: Sun Apr 10 2005 - 00:34:48 CDT

>
> >Lastly, has anyone carried out long and reasonable
> >Langevin simulation with Amber 8?

I looked at a 20 ns DNA simulation I ran, with the default nscm value.
I did the simulation in 1 ns "chunks", so there were 20 restarts. There was
certainly no overall translation or rotation...I have not yet looked for
any periodicities in the energies, but may do that. This was a 15-basepair
segment of DNA, with 950 atoms.

...dac

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