Hi,
One more note: if you look at the formula for the vibrational entropy
you will see that this function falls of quite sharply with increasing
frequencies. Hydrogen vibrations obtained from normal mode have
essentially no influence on the final entropy despite their, typically,
relative high proportion to all other normal modes. Just look at the
output from e.g. nmode to see this in action.
When you do quasi-harmonic analysis/PCA you are typically looking at the
large global motions i.e. low frequency modes. Hydrogens should have
very little influence on this, maybe you could see some effect from
C-alpha only versus heavy-atoms only (i.e. including the side-chains).
Maybe worth a try to get a feel for it.
Cheers,
Hannes.
On Tue, 28 Apr 2015 12:51:46 +0200
Josh Berryman <the.real.josh.berryman.gmail.com> wrote:
> >>I was thinking if maybe I could reduce the number of frames needed
> >>for
> the quasi-harmonic
> >>calculation by removing all hydrogen atoms from the trajectory.
>
> Absolutely, entropy from things like methyl-group rotation is probably
> unimportant and not very well captured by this method anyway. It is
> not unheard-of to throw away everything except the C-alphas,
> especially if memory for the diagonalisation becomes a problem.
>
> Also, try doing a convergence analyisis of what happens to the
> entropy as you run the calculation on increasingly longer trajectory
> segments, it should follow a power law which you can extrapolate to
> t=infinity. This rather obscure maths paper gives an explanation of
> why it works, plus links back to the simulation papers where the
> approach was discovered:
>
> Title = {Statistical inference for functions of
> the covariance matrix in the stationary Gaussian time-orthogonal
> principal components model},
> Author = {Dryden, IanL. and Kume, Alfred and Le,
> Huiling and Wood, AndrewT.A.},
> Journal = {Annals of the Institute of Statistical
> Mathematics},
> Year = {2010},
>
>
>
> >>I started an MMPBSA calculation using these three trajectories and
> >>using all 250 000 frames and at the rate at which the frames are
> >>being processed right now, I anticipate at least 3-4 days will be
> >>spent just on the GB calculations
>
> The number of nanoseconds might be more pertinent than the number of
> frames here. Collecting a PE snap every 2 femtoseconds would
> certainly be a bit excessive, as the decorrelation time of your
> energies is rather longer than this.
>
> >>restarting MMPBSA...
>
> sorry, never tried
>
> Josh
>
>
>
> On 27 April 2015 at 05:35, Laura Tociu <ltociu.princeton.edu> wrote:
>
> > Dear Amber users,
> >
> > I am attempting to calculate the entropic contribution to the
> > binding energy of a very large system and previously I had thought
> > about truncating the system and using NMode but eventually decided
> > against it because the protein has a very obvious correlated motion
> > of its monomers and upon binding that motion is almost lost so the
> > quasi-harmonic approximation would probably be pertinent to this
> > case.
> >
> > The number of atoms being 6000 + I need at least 18 000 frames for
> > the quasi-harmonic approximation. So I now have three separate
> > trajectories (one of the protein, one of the complex and one of the
> > ligand -- I wanted to use separate trajectories precisely because
> > upon binding the motion of the protein changes), each having 250
> > 000 frames.
> >
> > I started an MMPBSA calculation using these three trajectories and
> > using all 250 000 frames and at the rate at which the frames are
> > being processed right now, I anticipate at least 3-4 days will be
> > spent just on the GB calculations, and I can't estimate how much
> > the entropy calculation will take and whether everything will run
> > smoothly or not from now on.
> >
> > Since obtaining this entropy is a little time-sensitive now, I was
> > thinking if maybe I could reduce the number of frames needed for
> > the quasi-harmonic calculation by removing all hydrogen atoms from
> > the trajectory. This would reduce the number of frames needed by
> > roughly a half. I was thinking about doing two MMPBSA calculations:
> > one using a trajectory with all of the hydrogens present, from
> > which I would derive the intramolecular energy and the solvation
> > energy and one using a trajectory that is free of hydrogens, from
> > which I would simply derive the entropy. I recall reading about
> > something similar in an article but am not sure I remember
> > correctly. Is this a valid procedure?
> >
> > If not could someone tell me if an MMPBSA calculation can be
> > restarted if it dies for whatever reason and how? I know there is
> > an option to use the existing input files, but I am not sure if
> > this means that the script will pick up where it left off if it
> > died in the middle of frame processing for example.
> >
> > Thank you!
> >
> > Laura
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Apr 28 2015 - 04:30:05 PDT
