code implementation based on NAMD source code

From: Teerapong Pirojsirikul (
Date: Thu May 29 2014 - 17:39:21 CDT

Dear NAMD users,

I would like to implement some code based on NAMD source code. Right now,
I'm trying to understand how the code works step by step. I have specific
questions on how the code reads in parameters from a configuration file. As
I understand, there is the class ConfigList that is in charge of reading
and storing keywords from the configuration file. The 'add_element'
function in the class creates new objects that store keywords/parameters
defined in the configuration file. This list of parameters will be later
used in the code. However, it is not clear to me how this function is
explicitly invoked in the code and in which step that the parameters from
configuration file are read and stored. In ConfigList.C, there is a comment
'The scripting interface will call our add_element routine'. By the word
'scripting interface', does this mean scripting language such as tcl
language that is being used with NAMD? Does this also imply that the
add_element function is somehow invoked and handled by some related tcl
function/command in the code?

Any suggestions would be greatly appreciated.


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