VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 25 2012 - 11:10:26 CDT

Yes.

Open the file before you initialize bigdcd, assign it to a variable that you declare and import as global.
Make sure you close the file when closing down bigdcd, so you don't lose anything through file buffering.

Axel. 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
-----Original Message-----
From: flavio seixas <oivalf_nix_at_yahoo.com>
Sender: owner-vmd-l_at_ks.uiuc.edu
Date: Tue, 25 Sep 2012 08:16:29 
To: VMD List<vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Big DCD file help
Hi,
I am trying to calculate rmsd from my dcd files. The namd rmsd tcl script is working fine. Unfortunately the values appears listed in tk window and can not be copied at all.
Is possible to put the rmsd values in a file?
This is my script:
proc myrmsd { frame } {
   global ref sel all
   $all move [measure fit $sel $ref]
   puts "$frame: [measure rmsd $sel $ref]"
 }
set mol [mol addfile CALDHmT178_wb_min4.pdb type pdb waitfor all]
set all [atomselect $mol all]
set ref [atomselect $mol "name CA" frame 0]
set sel [atomselect $mol "name CA"]
bigdcd myrmsd dcd CALDHmT178_wb_eq5.dcd
bigdcd_wait