Hi Aron,
thank you very much!
I'll try to play with those options. BTW using quasi-hormonic analysis for
the entropy calculations for the same systems I've obtained wrong entropy
(which was very high!).
Kind regards,
Gleb
2014-12-03 15:50 GMT+01:00 Aron Broom <broomsday.gmail.com>:
> 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
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Aron Broom M.Sc
> > > PhD Student
> > > Department of Chemistry
> > > University of Waterloo
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
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> > 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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Received on Fri Dec 05 2014 - 04:00:02 PST
