AMBER: about coordinates ****** and diffusion

From: kepa koldo burusco <>
Date: Sun, 28 Jan 2007 18:15:57 +0100 (CET)


Hello Mr. Case (and amber users),

The simulations I was running were a 5 nanoseconds
ones. Fortunately, in the end, I was able to calculate
diffusion constants without any problem (what was
really my goal).

But now you have mentioned the problem related to
rapid diffusion on short time scale, I realised about
a "strange" behaviour of the mean-square-displacement
(MSD) paremeter on friday evening: The MSD plot versus
time was really amazing. As time advances the MSD
value grows even fastly. I expected a "reasonably"
linear behavior of MSD versus time as the slope is the
Diffusion Coefficient. Instead, I obtained an almost
"quasi-perfect" parabolic shape with no traces of
fluctuations at all!!!

My first guess was that I had choosen the wrong column
when ploting the data since ptraj produces 5 different
outputs: "x", "y" and "z" individual MSD, 3D-MSD, and
sqrt(3D-MSD). I checked that point and I confirmmed I
had taken the right one, the 3D-MSD (the quadratic
one) to use the equation: d/dt (MSD) = 6D.

Then, do you think the results I got are not
trustworthy at all? Any idea why they went wrong?

I would really appreciate any suggestion you could
send me about this topic.

By the way, I am still using amber7, both serial and
parallel versions.

Thank you very much in advance.

Kepa K. Burusco

PhD Student
Universidad Autónoma de Barcelona

--- "David A. Case" <> escribió:

> On Tue, Jan 23, 2007, kepa koldo burusco wrote:
> >
> > I'm running ptraj and carnal calculations over a
> > trajectory file: RMSD, Radius of Gyration,
> > Diffusion... using AMBER 7.
> >
> > The original calculation is a NPT Molecular
> Dynamics
> > in CHCL3 solvent and box is a truncated octahedron
> (by
> > the way, I am not removing the solvent molecules).
> >
> > My problem is that restart file (the reference
> > structure) for RMSD calculations shows a few lines
> > like the next ones:
> >
> > -59.4669830-843.8849945 568.4678259
> > -61.0471413-843.3087710 567.9562990
> > -59.1762415-845.5550610 568.0020731
> > -59.1694863-843.5231680 570.1622704
> > 23.1586695************ 614.6020183
> > 22.5738716************ 615.3055373
> Unfortunately, there is not much you can do to fix
> the restart file. You may
> still be able to analyze the trajectory file, since
> it handles overflow
> somewhat more gracefully, (although I don't know if
> that was true in Amber 7
> or not....)
> How long was the simulation? If you are getting
> very rapid diffusion on short
> time scales (say a few nanoseconds) it might an
> indication that something is
> wrong.
> More recent versions of Amber handle this problem in
> a better way (although
> still not completely satisfactorily....)
> ...good luck..dac
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Received on Wed Jan 31 2007 - 06:07:08 PST
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