AMBER Archive (2008)

Subject: AMBER: self-diffusion coefficient and Berendsen

Date: Fri May 23 2008 - 03:03:49 CDT

Dear members,

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
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 ?

Thank you,

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