Hi James,
I've mostly ended up using the Quasi-Harmonic method for the entropy, as
the NMA takes a very long time for each snapshot when you have a larger
system. But when I did use it, I also saw a similar output. It seems like
it wants to be run for more steps of minimization (probably because your
system is larger than maybe the typical test systems were) and at this
point hasn't stopped being able to reduce the energy. Under the &nmode
namelist thing in the input file, you can give a value for maxcyc, which
defaults to 10,000. Keep in mind, increasing the number of cycles, and
adding more snapshots is going to mean a lot more computational time used.
I would suggest, while that is running, to try out the quasi-harmonic
option. It will give the same output, and also breakdown the entropy to
the same terms, but will complete much faster. Also, from the minimal
reading I've done on the subject, it didn't seem like the normal modes
analysis was a clear cut winner in terms of the results, at least for
protein sized systems. Maybe someone with more experience and
understanding can comment on that?
~Aron
On Wed, Dec 3, 2014 at 3:15 AM, James Starlight <jmsstarlight.gmail.com>
wrote:
> Hi Aron,
>
> thank you very much for the suggestions! I'll try to re-calculate my
> calculations using different number of input snapshots. Also in the
> progress.log I've found many bellow errors on different steps of the
> enthropy calculations using NMA
> Line minimizer aborted: step at upper bound 0.052119948
> Line minimizer aborted: step at upper bound 0.035221234
> Line minimizer aborted: step at upper bound 0.012871543
> Line minimizer aborted: step at upper bound 0.025078351
> Line minimizer aborted: step at upper bound 0.0053674051
> Line minimizer aborted: step at upper bound 0.0032108337
> Line minimizer aborted: step at upper bound 0.027091995
> Line minimizer aborted: step at upper bound 0.00039482436
> Line minimizer aborted: step at upper bound 0.00028552353
> Line minimizer aborted: step at upper bound 0.0023149984
> Line minimizer aborted: step at upper bound 0.003469208
>
> Is it possible to modify some parameters for the minimization to suppress
> those errors as well?
>
> Thanks for help,
>
>
> James
>
> 2014-12-03 0:35 GMT+01:00 Aron Broom <broomsday.gmail.com>:
>
> > you should be able to see from the MMPBSA output log, where the errors
> are
> > coming from. I believe the NMA code will actually also warn you about
> > likely problems (assuming you are using the lastest AmberTools). For
> > instance, typically you want in the range of 1 snapshot per degree of
> > freedom. So, depending on whether you had hydrogens fixed or not, you
> > could be looking at ~2-3 times the number of non-water atoms, which I
> > imagine for your system is going to mean you want in the range of 10,000
> > snapshots. But, you also want those snapshots to be independent of each
> > other, that is, not correlated. So you probably can't go lower than
> taking
> > a snapshot every 10ps or so. Which, oddly enough, would mean about
> 100ns,
> > which is what you have. So, yes, you could improve your error by
> recording
> > snapshots as frequently as say 10ps. This will also, by default, reduce
> > the error from the enthalpy portion of the calculation, since the error
> > will decrease with the square-root of the number of measurements
> (assuming
> > again that they are independent, and also that you are in fact exploring
> > within the global energy minimum).
> >
> > On Tue, Dec 2, 2014 at 4:29 PM, James Starlight <jmsstarlight.gmail.com>
> > wrote:
> >
> > > Dear Amber users!
> > >
> > > Performing several mmgbsa calculations (with NMA for enthropy
> > calculations)
> > > for my test systems I've noticed significant error corrections in the
> dG
> > > found in final result. From the below log you can find that the order
> of
> > > such corrections in both cases are equal to the calculated values.
> Here I
> > > used 100 ns trajectory of the production run of the membrane protein
> > system
> > > as the input for mmgbsa; totally using 50 snapshots both for the
> entalpy
> > > (each snapshot has been taken every 250000 steps) as well as for the
> > > entropy calculations.
> > > 1) Does the enthropy term make main contribution to the errors?
> > > 2) Is it possible to reduce its value (e.g using longest MD
> > > trajectories,choosing smaller sampling intervals or do better
> > minimization
> > > as well as method for hessian diagonalization in case of NMA)?
> > >
> > >
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > For system1
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > Using Normal Mode Entropy Approximation: DELTA G binding = -8.1087
> > +/-
> > > 5.8570
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > For system 2
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > Using Normal Mode Entropy Approximation: DELTA G binding = -10.3566
> > +/-
> > > 7.7316
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> > > Thanks for suggestions,
> > >
> > > James
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Dec 03 2014 - 07:00:02 PST
