From: Luis Gracia (
Date: Mon Apr 25 2005 - 19:29:21 CDT

Simon Whitehead said the following on 04/25/05 07:17:
> 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

Hi Simon,

which is exactly the problem? I guess we need some more info...


Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021
Tel: (212) 746-6375
Fax: (212) 746-8690