AMBER Archive (2007)

Subject: RE: AMBER: about coordinates ****** and diffusion

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Jan 28 2007 - 11:28:30 CST

Dear Kepa,

Are you calculating the RMSD of both the solute and solvent? If so then you
will see a gradually increasing RMSD as solvent molecules slowly drift away
from the central box. They are reimaged into the central box mathematically
but are written to the trajectory file as their original unimaged locations.
Hence they look like they are just gradually diffusing away from the solute
ofer time. You reimage your coordinate file using ptraj but even then if you
calculate the RMSD off all the solvent molecules as well you will see jumps
in RMSD as a solvent molecule diffuses out of one side of the box and
re-enters on the other side.

So check what mask you are using for the RMSD calculations.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of kepa koldo burusco
> Sent: Sunday, January 28, 2007 09:16
> To: amber_at_scripps.edu
> Subject: AMBER: about coordinates ****** and diffusion
>
> [28-I-2006]
>
> 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
> BARCELONA (Spain)
> **********************************
>
>
> --- "David A. Case" <case_at_scripps.edu> 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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>
>
>
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