From: Alex Liu (
Date: Wed Feb 23 2011 - 12:51:16 CST

Dear VMD users,

I have a few questions regarding RMSF feature in VMD:

1. I want to calculate RMSF for an atom. I need to align my molecule first. I
Know that using RMSDTT in VMD can do this for me. So, I just load the dcd file
and click align (ref is top molecule) in RMSDTT. Then I save as coordinated
(dcd) and reload in VMD or I can also load the initial structure and then load
the trajectory file and choose the first structure as ref and click align and
then save the coordinates of the second structure .Then I can use:

 set outfile [open rmsf.dat w]
 set sel [atomselect top "name CA"]
 puts $outfile "[measure rmsf $sel first 1 last 1500 step 1]"
 close $outfile

as shared on the website to measure RMSF on that atom. Is this correct? Because
the RMSF value I am getting is very different from what I expect to see.

2. I Know that using VMD one cannot measure RMSF for a group of atoms (example:
center of mass of some atoms). Is there any suggestion how to do this?