VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon May 02 2016 - 09:46:11 CDT

there also are multiple plugins with functionality related to this, e.g.:

http://www.ks.uiuc.edu/Research/vmd/plugins/rmsdtt/
http://www.ks.uiuc.edu/Research/vmd/plugins/rmsdvt/

it is difficult to give a specific recommendation without knowing the context.

axel.

On Mon, May 2, 2016 at 10:23 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> Hi Devanand,
>
> This will require a script.
>
> #Load in the two dcds. Look up how to do this in the userguide under the
> "mol" command.
> set refid [mol new ...]
> ...
> set selid [mol new ...]
> #Make two selections. Note that the selected number of atoms should match!
> set ref [atomselect $refid "protein"]
> set sel [atomselect $selid "protein"]
> #The third selection is the one that gets moved to superimpose the
> trajectories
> set all [atomselect $selid "all"]
> if { [$ref num] != [$sel num] } {
> puts "unequal selection sizes. Fix you selections."
> }
> #Go through each frame, and align it
> for { set f 0 } { $f < [molinfo $refid numframes] } { incr f } {
> $ref frame $f
> $sel frame $f
> $all frame $f
> $all move [measure fit $sel $ref]
> }
>
> However, I have a question. Why would you want to do this? Usually
> trajectories diverge away from one another, and it makes just as much sense
> to align everything to a single reference.
>
> -Josh
>
>
> On 04/30/2016 04:29 PM, Devanand T wrote:
>
> Is it possible to superimpose 2 dcd files (with equal number of frames)
> frame by frame? If so, can someone help me on this?
>
> --
> regards,
> Devanand T
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.