RE: atom distances

From: Pijush Ghosh (
Date: Wed Jan 04 2006 - 15:14:53 CST

Hi Bo,
  Its not that difficult. You have your information stored in DCD file
already. Make an indexfile with only those two atoms and then use CATDCD to
extract the trajectories of those two atoms, load it in VMD, save it as pdb
file, and then write a couple of lines prog. either in excel or matlab to
find the distance between the selected atoms over time....
Does this work ?

Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA

-----Original Message-----
From: [] On Behalf
Of bo baker
Sent: Wednesday, January 04, 2006 2:17 PM
Subject: namd-l: atom distances

Hello, NAMD:

I would like to exam the distances between two charged atoms from a MD
run. How could I do this? I have search the mail list, and not easy to
find the answer. The VMD can do it by pick up the two targeted atoms.
But how can I get the all the distance value from the trajectories?

Thank you for your advice.


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:29 CST