Re: question related to rmsd

From: JC Gumbart (
Date: Mon May 05 2008 - 17:58:43 CDT

Then the answer is very simple. "frame0" is the reference. In your
case, it's the first frame of whatever the first trajectory you load is.

As for your followup, it's hard for me to say what's is responsible
for the drop. Regardless though, you should not be minimizing so
much. As you can see in the reference provided, minimization is only
meant to be performed for a couple of thousand steps at most, not for
hundreds of thousands of steps. However, the actual dynamics (run
___) should be longer.

On May 5, 2008, at 4:35 PM, snoze pa wrote:

> 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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