AMBER Archive (2005)

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

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 08 2005 - 12:48:27 CDT

On Fri, Apr 08, 2005, Peter Varnai wrote:
>
> I continue to look into the problem of quasi-periodic behaviour in
> Langevin simulations in Amber8. I created a small system to test different
> input parameters

How small is your system? The Langevin random forces that Amber uses have
no constraints to prevent overall rotation or translation from happening;
for fairly large systems, nothing too bad seems to build up, but I haven't
checked this all that carefully.

When a Langevin simulation is restarted, the random number generator goes
back to the beginning, so you get a re-run of the random forces that you would
have had from the previous run. You might try changing the "ig" variable
in different runs, to get a different stream of random forces, and see if that
affects the behavior you see.

...dac

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