[gmx-users] pull.pdo AFM force
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.
As an example, with one pulling group, and pulling in 3D, the output
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.
More information about the gromacs.org_gmx-users