From: Bharat Sharma (
Date: Wed Nov 12 2014 - 13:52:55 CST

Hello again,
I figured it out how to call functions to select atoms, but how to deal
with Periodic atoms and calculate hydrogen bonds within selection only?

Thank you.


On Wed, Nov 12, 2014 at 1:38 PM, Bharat Sharma <>

> 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.
> Bharat