Thank you for the reply, should have done more homework.

Made my simulations run 400x faster now and the results look good!!

Thank you so much!

Hi Peter, Ah, ok. What I want is exactly what you described. Average structure to me is taking the sample frames and finding the average structure (having trouble defining it further). I guess I could give the comparison of "law of large numbers". The more samples I have the more accurate the struct...

Sorry for the late response. 5.0 did not change the molecule from going out of periodic box.

Perhaps I did not install 5.0 correctly? But doubt it, I deleted the old 4.1 installation folder and put in 5.0.

Installed Ubuntu and AmberTools12. I have started XLEaP, loaded the .pdb I had, but when I try to generate the .prmtop and .inpcrd it gives an error. I know that this question belongs to the AMBER mailing list. I have posted a couple times there, but I only see my first question which does not apply...

For some reason when loading the old output it looks fine....can't reproduce results.

Was able to remove all water. Tried same simulation on laptop with ati gpu (vs desktop with nvidea) and it did not split into octants for some reason. When I get home I will test the .pdb with water disabled in vmd. Lastly, how would I change the .pdb below so that it reads it correctly? Obviously i...