[gmx-users] AFM pulling options

Marc Baaden baaden at smplinux.de
Fri Aug 2 11:16:55 CEST 2002

Hi again,

I sent the changes again to Justin. For those who might be interested
here is a brief summary:

I added an option 'afmdetail' to the pull parameters, which would lead
to more detailed output, especially with respect to getting force-extension
curves out of the simulation. The NEW option is

afmdetail                = yes

in pull.ppa.

- 5 values are output to pull.pdo:
  Force Springpos pull_grp_pos ref_grp_pos extension
  where    Force     = k * (Springpos-pull_grp_pos)
           extension = pull_grp_pos - ref_grp_pos

- in the Gromacs code for AFM pulling, the refgroup positions are not up-
  dated. I changed that for the case of afmdetail=yes, so that you can use
  these coordinates to calculate the extension.

- Note that the routine that writes AFM data to pull.pdo in Gromacs assumes
  that you pull in Z direction, as it only writes out the Z components of
  eg the forces. That is if you pull along y, you will get 0 forces written
  out although it seems that it was actually pulled along y. This is because
  the z component of the force is 0 when you pull along y.
  I couldn't figure out how to change that in a simple way, so even with
  afmdetail, it only works for Z-direction pulling

jlmaccal at ucalgary.ca said:
>> Hi Marc,
>> which changes were those?  I don't remember getting any, but that
>> doesnt' mean much ;)

  Marc Baaden

 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
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