VMD-L Mailing List

From: David Smith (dsmith37_at_nd.edu)
Date: Sun Mar 10 2013 - 14:33:17 CDT

Hello,

I am in dire need of timely assistance with a few post-processing routines
in NAMD/VMD. I have completed simulations on an ionic liquid in water, and
I am trying to perform the following:

1. Velocity autocorrelation function for the system: I am trying to develop
a Tcl scripting routine for VMD using the following resource as a reference
and to develop a logical pseudocode:
http://www.timteatro.net/2010/09/29/velocity-autocorrelation-and-vibrational-spectrum-calculation/.
As a side note, I'm not sure how I could get self-diffusivity from the VACF
for the ions themselves, as I only have one cation and one anion in a
system of hundreds of water molecules. Could you help me with this two-part
problem?

2. Spatial distribution function: Also, I am trying to compose a spatial
density/distribution function for a given reaction coordinate defined by
two heavy atoms, one on each ion of the ionic liquid. I am trying to figure
out the Volmap plugin, but I am having difficulty figuring out how to
implement the transform matrix option to use one atom of the reaction
coordinate as a reference position.

If you could at least get me started with this, that would be great. I must
admit that I am only an undergraduate student, and I have limited
experience with Tcl scripting and the higher concepts of statistical
mechanics. Thank you in advance!

Sincerely,

David Smith 

-- 
David Smith
University of Notre Dame
Chemical Engineering
Class of 2013
dsmith37_at_nd.edu
davesmith4398_at_yahoo.com
(484)802-4398