VMD-L Mailing List

From: Maria Antonieta Sanchez Farran (mfarran_at_engr.psu.edu)
Date: Sun Sep 23 2012 - 15:04:58 CDT

Hi Shiva,

You can extract coordinates by using the get { x y z} command in tcl. If
you apply this to an atom selection ($sel get {x y z}), you will obtain
a list of lists. Make sure that you manipulate lists appropiately using
the "lindex" command. If you are starting, manipulating lists can be a
bit confusing, so I would recommend you to get famililar with that
first. Take a look to this link - it explains this very clearly:
http://www.csb.yale.edu/userguides/graphics/vmd/ug/node181.html.

Another alternative, is to use MATDCD, which is a MATLAB package for
reading DCDs: http://www.ks.uiuc.edu/Development/MDTools/matdcd/

Hope this helps,
Maria Antonieta