Hello --

I would guess that your analysis and comparison would benefit from statistical tests to determine the significance of the difference in the presence of the errors you observe.  This will allow you to answer your question about the reliability of your results.

Good luck,

Nathan

On Dec 4, 2009, at 8:39 AM, Dimitrios Spiliotopoulos wrote:


Dear prof Baker,

the standard deviations for my calculations are now lower than before (around 30% of the mean value, very similar in absolute terms between the wildtype and the mutant complexes).
I calculated the DeltaDeltaG values (by that I define the difference of the mutant DeltaG and the wildtype DeltaG) of a number of mutants, obtaining a fairly good correlation. These standard deviations are nonetheless higher than the DeltaDeltaG values, thus possibly invaliding any correlation.
Does this nullify my results or are they still reliable?

Thank you very much!!!

Dimitrios Spiliotopoulos

_________________________________________________________________________________________________
Dulbecco Telethon Institute c/o DIBIT Scientific Institute
Biomolecular NMR Laboratory, 1B4
Via Olgettina 58, 20132 Milano (Italy)
Tel     : 0039-0226434348/5622/3497/4922
Fax    : 0039-0226434153
Email : spiliotopoulos.dimitrios@hsr.it; dimitris3.16@gmail.com
Skype: dimitris3.16









2009/7/30 Nathan Baker <baker@biochem.wustl.edu>
Hi Dimitrios --

Such variance is fairly standard in polar solvation energies.  Part of the "problem" is related to sensitivity in the sharp dielectric boundary while part of the issue is related to the intrinsic conformational sensitivity of polar solvation.  I'm not sure that such variance really is all that surprising.  You could try a smoother dielectric boundary (e.g., splines) but please be aware that these require specialized parameters.

Thanks,

Nathan

On Jul 29, 2009, at 10:12 AM, Dimitrios Spiliotopoulos wrote:


Hello APBS users!

I have a question about the standard deviations values of my simulation-derived structure files of a protein interacting with a peptide.

I performed five simulations (each composed of 1 ns NVT equilibration and a 3 ns NPT production run) and pasted them together in order to get a single "overall" simulation. On this latter simulation, I performed the MM/PBSA calculations.
I noticed that the polar solvation contribution had standard deviations that are 1- to 3-fold the mean value (e.g., -36.8534 +/- 78.0839 kJ/mol or -88.9041 +/- 88.6444 kJ/mol), whereas my apolar solvation contribution has more reasonable results (the standard deviations are 3-5% of the mean values). I thought may be the conditions were too permissive and my simulation was oversampling, so I changed them into 100 ps NVT and 100 ps NPT. Thus, I calculated the values for all the frames (1000) or every 10 frames (100), but I had very similar results.

I cannot figure out why the standard deviations of the polar solvation term are so high: is there any parameter in the polar solvation calculation input file that can affect this?

Thank you very much in advance!

Dimitrios Spiliotopoulos

_________________________________________________________________________________________________
Dulbecco Telethon Institute c/o DIBIT Scientific Institute
Biomolecular NMR Laboratory, 1B4
Via Olgettina 58, 20132 Milano (Italy)
Tel     : 0039-0226434348/5622/3497/4922
Fax    : 0039-0226434153
Email : spiliotopoulos.dimitrios@hsr.it; dimitris3.16@gmail.com
Skype: dimitris3.16


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Nathan Baker (http://bakergroup.wustl.edu/)
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Computational and Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis