From: Bharat Sharma (
Date: Wed Nov 12 2014 - 12:38:19 CST

Hello Experts,

I am interested in doing some MSD analysis for subset of my simulation box.
Basically I want to call different functions on TCL window. I have some
questions regarding calling VMD subroutines on TCL window.

How do I call the functions to do following tasks?
1) to call selected atoms (for example: name O within 3 of index 123)
2) number of hydrogen bonds within selection
3) MSD of selected systems.

Any suggestions are expected very helpful and appreciated.

Thank you.