From: Nicholas Musolino (
Date: Fri Aug 20 2010 - 12:46:36 CDT

Hello Hirdesh,

Have you seen the VMD tutorial?

And in particular the "Data ANnalysis" section?

If you read through the "Example of an analysis script," you should be able to change the relevant part to calculate RMSF.

Hope this helps!

Nicholas Musolino

On Aug 20, 2010, at 12:22 PM, hirdesh kumar wrote:

> Hi All,
> I have the AMBER files in .crd and .parm7 format and I am looking forward to calculate the rms fluctuation residue wise during the entire run.. Please tell me how can I calculate the rmsf using VMD1.8.7 version.
> Thanks in advance,
> Hirdesh

Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT | 617-253-6675 | Room E19-528