From: Simon Whitehead (
Date: Mon Apr 25 2005 - 06:17:35 CDT

Hi everyone,
Firstly, thanks for the help in loading my amber MD files into VMD! My 1st 500ps simulation has just completed so am keen to start analaysing the data but have been unable to get the RMSD tool to work. I have loaded a PARM file plus a coordinate file (crdbox) containing coordinates for the entire 500ps dynamics simulation but am not sure why i cannot run the tool and calculate the RMSD values over this time period. I would appreciate your help on this matter.
Many thanks
Simon Whitehead