AMBER Archive (2008)

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

From: Jennifer.Thomas_at_cbt.uhp-nancy.fr
Date: Sun May 25 2008 - 05:47:22 CDT

Hi !
I had put the value of NSCM greater than the number of steps because I didn't
know why it can be useful and it was creating discontinuities on the total
energy profile. But after reading the 'Flying Ice Cube', I put it back to its
default value and now the diffusion coefficient is ok with Berendsen thermostat
too.
As the diffusion coefficient depends upon the temperature, isn't it a problem to
calculate it from a NVE simulation ?
Thanks to both of you !

Jennifer

Selon "David A. Case" <case_at_scripps.edu>:

> On Fri, May 23, 2008, Jennifer.Thomas_at_cbt.uhp-nancy.fr 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
> information.
>
> ...dac
>
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