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.



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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