From: Pedley, Anthony M (apedley_at_purdue.edu)
Date: Tue Jun 25 2013 - 09:15:33 CDT

I have been trying to calculate RMSF values for C-alpha atoms from a MD simulation performed in Desmond. I have loaded the files and then used the Timeline analysis tool to analyze the data set. The problem is that the MD simulation was run in an explicit solvation model, and the trajectory files are not aligned. When I use Timeline to calculate RMSF values, I get huge (60 angstrom) jumps in the RMSF values over time. I know that this cannot be the case from my own structural analysis.

Does anyone know of a way that I can align the protein in all trajectory files so that it reports the correct RMSF values in Timeline? Or is there a better way to achieve the same output?

Thanks,
Tony Pedley
Purdue University