Hey Naser,
First - comment on the paper - If you do a citation search on who cited
that paper, you will come across with a couple of papers that also
discuss the whole equilibrium phenomenon so I should have been more open
to point this paper as a starting point.
Second - on eigenfrequencies -
Brooks, B. R., D. Janezic, and M. Karplus. 1995. Harmonic analysis of
large systems. I. Methodology. Journal of Computational Chemistry
16:1522-1542.
Janezic, D., and B. R. Brooks. 1995. Harmonic analysis of large systems.
II. Comparison of different protein models. Journal of Computational
Chemistry 16:1543-1553.
Janezic, D., R. M. Venable, and B. R. Brooks. 1995. Harmonic analysis of
large systems. III. Comparison with molecular dynamics. Journal of
Computational Chemistry 16:1554-1566.
and the papers cite these - a really nice resource on NMA and QH
On Sat, 2009-06-27 at 14:19 -0400, Naser Alijabbari wrote:
> I have attached the RMSd plot from a 400ps NVE simulation of a protein with
> 108 residue. The plot is similar to the one in the paper but when I plot the
> eigenfrequencies (from quasiharmonic analysis) every 10ps, around 350ps
> something, which I don't know how to characterize, happens and the
> eigenfrequency which were similar between previous 10ps intervals, change
> dramatically. So ETOT and RMSd might not be enough to know that something
> odd is happening.
>
> On Sat, Jun 27, 2009 at 10:29 AM, Cihan Aydin <cihan.aydin.umassmed.edu>wrote:
>
> > I encountered this e-mail while roaming on the reflector. I'll cite a
> > paper that helped me much.
> >
> > Stella,L.; Melchionna,S.
> > J. of Chem. Phys., Vol. 109, No.23, 1998
> >
> > Cheers,
> >
> > Cihan
> >
> >
> > On Thu, 2009-05-28 at 14:15 -0400, Carlos Simmerling wrote:
> > > that's way too general. it depends on many things, such as the quality of
> > > the experimental structure, the difference in conditions between your
> > > simulation and the experiment (pH, solvent, ions etc) and where in the
> > > structure the rmsd values come from. rmsd is a very broad measure and a
> > > value of 2 may mean that all regions differ by about 2, or that many
> > differ
> > > by 1 and others differ by a larger number (for example 5, or maybe 10).
> > rmsd
> > > itself is only 1 measure of simulation quality so I strongly disagree
> > that
> > > simulation rmsd values should "not be greater than 2". if you do get
> > larger
> > > values, though, you should find out why and see if there is a way to
> > > validate that the behavior is reasonable.
> > >
> > > equilibration can be very tricky and there is no one "correct" protocol
> > we
> > > can give. it depends again on the initial structure and any differences
> > in
> > > your simulation conditions from the expt. it is entirely possible to have
> > > most of the structure look ok, but due to bad placement of an H atom or
> > even
> > > an ion, part of the initial structure will be incorrectly modeled and the
> > > simulation will not give a good model. equilibration can help with these
> > but
> > > you need detailed information about differences between MD and experiment
> > to
> > > proceed. we tend to be cautious and use about 10 steps in our general
> > > equilibration procedure, and more when anything was modeled (such as a
> > side
> > > chain or a ligand).
> > >
> > >
> > > On Thu, May 28, 2009 at 2:08 PM, nicholus bhattacharjee <
> > > nicholusbhattacharjee.gmail.com> wrote:
> > >
> > > > Thank you Bill. But you did not answer my second question. Is the rmsd
> > > > value
> > > > between the initial structure and the final structure be not more than
> > 2
> > > > Armstrong.
> > > > _______________________________________________
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> > --
> > Cihan Aydin
> > UMass Graduate School of Biomedical Sciences
> > PhD Student . Schiffer Lab
> >
> > 364 Plantation St. LRB 970M
> > Worcester, MA 01605
> >
> > cihan.aydin.umassmed.edu
> > +1 (508) 856-3430
> >
> >
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> >
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--
Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student . Schiffer Lab
364 Plantation St. LRB 970M
Worcester, MA 01605
cihan.aydin.umassmed.edu
+1 (508) 856-3430
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Received on Mon Jul 06 2009 - 12:08:46 PDT
