[gmx-users] pull.pdo AFM force

Emily Walton ewalton at MIT.EDU
Tue Mar 14 18:35:16 CET 2006

> Hi all
> I have a short question.  Could you please tell me what do the  
> columns in pull.pdo (output file from AFM) stand for.  Is there a  
> simple way to obtain forces from AFM pulling? Thank you for help.
> Michal

As an example, with one pulling group, and pulling in 3D, the output  
columns read:

Time, Reference group X, Reference group Y, Reference group Z, Pull  
Group X, Pull Group Y, Pull Group Z, Spring X, Spring Y, Spring Z

for a total of 10 columns.

If you didn't pull in 3D, you'll only get output for the dimensions  
where pulldim was set to Y in your .ppa file. I'm not sure how  
multiple pull groups are handled.

I have a script to calculate the forces for pull runs using only one  
pull group in 3 dimensions that I can share on request.

-Emily Walton

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