AMBER Archive (2008)

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

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Fri May 23 2008 - 04:22:57 CDT

Hi,
> 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 ?
There are, for short, have a look at:
http://en.wikipedia.org/wiki/Flying_ice_cube

I hope that helps,
good luck
Andreas

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