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!
Spiliotopoulos _________________________________________________________________________________________________ Dulbecco Telethon Institute c/o DIBIT Scientific Institute
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