[gmx-users] pull.pdo followup

Emily Walton ewalton at MIT.EDU
Tue Mar 28 18:07:01 CEST 2006


I posted the following message a few weeks ago and just noticed that  
I was wrong. The column order is actually:

Time, Ref. X, Ref. Y, Ref. Z, Pull X, Spring X, Pull Y, Spring Y,  
Pull Z, Spring Z

Not intuitive, but it does make it very easy to make sure your spring  
starts in the same position as your pull group :)

This doesn't change anything about my script, so those of you who  
have it, don't worry, the script is right. It was just an error in  
the previous post.

-Emily Walton

> > 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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