AMBER Archive (2007)

Subject: AMBER: Statictical significance of differences in energy mean values between different simulations

From: Mostafa Sadighi (sadighi_amb_at_yahoo.com)
Date: Sat May 19 2007 - 10:54:40 CDT

Dear Amber Community,
   
  I have used ANAL to calculate the energy mean values between particular sub-systems during the whole trajectory and need to compare it with the same results in a different temperature.
   
  In the literature, usually if the differences between energy mean values in two different simulations were grater than the related standard deviations, the differences considered to be notable (for example mean-1 = 30 kcal/mol SD-1 = 2 kcal/mol, mean-2 = 27 kcal/mol SD-2 = 2 kcal/mol). But there are also some articles in which the authors report and discuss the differences in the mean values that are smaller than their related standard deviations (for example mean-1 = 30 kcal/mol SD-1 = 10 kcal/mol, mean-2 = 27 kcal/mol SD-2 = 10 kcal/mol).
   
  I will be thankful if someone explain me how one should determine the statistical significance of differences in energy mean values between different simulations.Why standard statistical methods (like calculating p-value) do not be used to determine statistical significance in such studies?
   
  Regards,
   
  Mostafa Sadighi

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