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
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> AMBER.ambermd.org
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>
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Received on Wed Dec 03 2014 - 00:30:02 PST
