[gmx-users] Question about COM-Pulling

[chris.neale at utoronto.ca]

Dear Christian:

As per my original comments, please provide a .mdp file, sample  
output, and all the other things that I asked for.

Chris.

--original message--

this is a more general question.

I thought that in analogy to an AFM-experiment a "dummy"-particle is placed
at a certain distance from the center of mass of the pull group (compare
figure 6.1 in the manual).
The force is then calculated as the displacement between the pulled atom
and the
"dummy"-particle. So if this is true which I'm not sure of,
I was wondering why the position of this "dummy"-particle is not plotted.

Or does this umbrella pulling work in a different way? How is the force
calculated?

Thanks a lot,
Christian

----------------------------------------------------------------------
The position of the reference group and the displacement of the pulled
group from the reference group should be printed (although perhaps
without the reference position if you are using absolute coordinate
pulling, which is not recommended anyhow).

If you want some better advice, please be more specific and include
cut and paste sections saying "I expected X at Y, but it was not in
the file Z.xvg". you should also include your pull-code .mdp options
and your grompp and mdrun commands.

Chris.

-- original message --

Dear users,

I've got a short question regarding com-pulling. From what I understand
Umbrella pulling is the same as AFM pulling using a harmonic potential.

Why is the position of the spring in the pullx.xvg not printed? One can
only find the vector between both pull groups. I looked into older
Gromacs manuals and in versions < 4 it seems as if this data is printed
to the pullx.xvg file or something similar.

With kind regards,
Christian