From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 17 2011 - 09:38:19 CDT
On Tue, May 17, 2011 at 10:16 AM, Jacopo Sgrignani <sgrigna_at_sissa.it> wrote:
> Dear all
> Im' using the VMD script trajectory_path.tcl and it works fine,
> however i would like to print the coordinates
> of the center of mass trajectory to a pdb (or another VMD readable
> file), could anybody help me?
the easiest way is to modify the script to write out an .xyz formatted file.
just right before the "return $gr_list" insert the following code (untested):
set fp [open comtraj.xyz w]
foreach coord $coords {
foreach {x y z} $coord {
puts $fp "1\nc.o.m.\n M $x $y $z"
}
}
close $fp
you may have to tweak some details, but that should
show you the principle.
cheers,
axel.
each iteration in the loop print out three lines:
1
center of mass
M $coords
and then
>
>
> thanks
>
> Jacopo
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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