[gmx-users] pull.pdo AFM force

Soren Enemark soren.enemark at polimi.it
Wed Mar 15 16:29:43 CET 2006

 Hi Emily,
 sometimes one can be quite lucky..:) I have just done a few simulations 
 in which I try to pull two molecules apart. I want to calculate the
 force as a function of intermolecular distance, and I just saw your
 post. Can I ask you for the script that you mentioned?


Quoting Emily Walton <ewalton at MIT.EDU>:

> > 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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