Re: custom pulling path

From: Leandro Martínez (
Date: Wed Apr 19 2006 - 14:16:36 CDT

Hi Raul,
I have written a script for doing that using the tcl interface of
NAMD. I have done some simulations, but my results are not published
yet. Here I send you the script. Appart from the namd configuration
file, you will need two files: one deffining the atom to be pulled,
the force constant and some other parameters, and a simple pdb file
containing the trajectory. The way the force is applied is written in
english yet (it is in portuguese, if it useful to you).

Here I send you three files: script2.tcl, script1-parameters.tcl and
halfpath.5.pdb, which are the script file and the to input files
required. The pdb file if only for deffining the points of the
trajectory and the parameter file is quite simple. The way to call the
script in your namd intput file is written in the header of the
script2.tcl file. This header refers to another script (script1.tcl),
but you will not need it.

The script is not extensivelly tested yet, but I believe it is working well------=_Part_11956_14703538.1145474196216--

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