Re: question related to rmsd

From: snoze pa (
Date: Mon May 05 2008 - 16:35:21 CDT

I am using the rmsd.tcl script in vmd. As in my next mail i sent one
attachment. I am not sure if I am right but the rmsd values are
calculated using rmsd.tcl script.. also shown below. I am running it
after loading minimization/ equilibration /fullmd run dcd files.

set outfile [open rmsd.dat w]
set nf [molinfo top get numframes]
set frame0 [atomselect top "protein and backbone and noh" frame 0]
set sel [atomselect top "protein and backbone and noh"]
# rmsd calculation loop
for { set i 1 } { $i <= $nf } { incr i } {
$sel frame $i
$sel move [measure fit $sel $frame0]
puts $outfile "[measure rmsd $sel $frame0]"

close $outfile

On Mon, May 5, 2008 at 4:19 PM, JC Gumbart <> wrote:
> It depends on how you do it. Are you using a script? One of the tools?
> Either way, you can control what the reference is. If it's still not clear,
> could you be more specific on how you're doing it and include any relevant
> scripts, etc.?
> On May 5, 2008, at 3:03 PM, snoze pa wrote:
> > Dear NAMD users,
> > I am using vmd to calculate the rmsd from my simulation. I have a
> > question related to rmsd calculations. what is the rmsd values! Is it
> > relative to minimized protein structure or to the original crystal
> > structure? Thank you very much for your suggestions.
> > s
> >

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