AMBER Archive (2008)

Subject: Re: AMBER: self-diffusion coefficient and Berendsen

From: David A. Case (
Date: Sat May 24 2008 - 15:20:27 CDT

On Fri, May 23, 2008, wrote:
> I'm doing self-diffusion coefficient calculations on a 50 ps dynamic of a
> box of 216 water molecules in NVT. When using NTT = 1, the Ptraj program
> gave a divergent coefficient. I switched NTT (and that's the only thing I
> changed) to 2 and then I got the expected result (around 3.5 10-9 m2/s). So
> I'm asking you, are there some known issues with the dynamic properties when
> using the Berendsen thermostat ?

Andreas pointed out some reasons that ntt=1 can go wrong, but they seem
unlikely in a system of pure water at 50ps. For dynamical properites, in
general you need to run NVE simulations, but ntt=1 with the default value of
tautp should not lead to problems (assuming that you have started with a
well-converged water box to begin with).

I suspect that something else is going on, but can't tell without more


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)