Re: [AMBER] MMPBSA: general question

From: Adrian Roitberg <>
Date: Tue, 07 Jun 2011 19:01:15 +0200

well, for starters, look at the fluctuations in the values for free
energy for the two runs. the difference between the two runs can ONLY be
thought of as large or small in regards to the absolute value of free
energy AND the fluctuations.

For instance, if the value of DeltaG_1 is -100+-2 and DeltaG_2 is
-102+-2, then you are talking about a difference of 1 % and the
distribution of free energies being overlapped between the two
calculations. It would be hard to imagine the method being better than that.

If in the other hand the values are DeltaG_1 is -5+-0.2 and DeltaG_2 is
-7+-0.2, then I would worry.

While I am standing in my pulpit, let me go back to one of my pet
peeves: "The systems are properly equilibrated." is not a a correct
statement. At least you have not written "The systems are fully

The nature of the methods and the systems we study precludes the idea of
equilibration. We do the best we can, but if we truly had an
equilibrated system (i.e. where EACH conformation is present according
to its own Boltzmann weight), then we would not have to do mmpbsa or
anything else. We would already have the answer to any question we wanted.

I am not sure yet what the proper term should be, but we should maybe
use 'The systems are sampled in the same way.' or something like that.


On 6/7/11 6:51 PM, George Tzotzos wrote:
> Hi everybody,
> Having run to independent 10ns production runs on the same protein/ligand complex, I observed a difference in Delta G binding of ~ 2kcal/mol. The systems are properly equilibrated.
> The above difference strikes me as too large. Is this something to be expected?
> Regards
> George
> _______________________________________________
> AMBER mailing list

                            Dr. Adrian E. Roitberg
                              Associate Professor
                Quantum Theory Project, Department of Chemistry
                            University of Florida
on Sabbatical in Barcelona until August 2011.
AMBER mailing list
Received on Tue Jun 07 2011 - 10:30:03 PDT
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