[gmx-users] Force Distance Curve from .trr .xtc

VENKATESH HARIHARAN vuh105 at psu.edu
Mon Aug 4 17:06:12 CEST 2008

     After running an AFM or Constraint pull simulation, I am looking to
generate a force distance curve between the pulled group and the reference
group.  Any suggestions on how to do this?  Currently I am doing it manually by
generating a .pdb movie of the entire pulling, and extracting the distance
between the two groups via coordinates in the .pdb at specified time points. I
then compare the distance at that time point with the force for that time point
in the .pdo file.  As you might imagine, this is very time consuming.  Does
Gromacs have a command to do this for you?  Thanks.


Venkatesh Hariharan
Pennsylvania State University
Schreyer Honors College
Undergraduate - Bioengineering

"You must be the change you wish to see in the world."
--Mohandas Karamchand Gandhi

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