[gmx-users] AFM pulling rate

Malin Bergenstråhle malbe at kth.se
Thu Aug 14 08:30:35 CEST 2008


The unit of the afm_rate in the GROMACS manual 3.3-1 is nm/ps.
I have read something in an earlier thread on this list that this might 
be a typo, it should be nm/timestep. Does anyone know? I would be happy 
if I could have that information.

Moreover, I am a bit confused about the output in the .pdo-file.  In the 
description of  .pdo-files on page 113 in the manual 3.3.-1 it is 
written that the .pdo file will contain calculated forces from 
AFM-pulling simulation. On the other hand, on page 118, the description 
of the AFM output is that it only contains positions of reference group, 
pulled group and spring. This is also the only information I can find in 
my output. I wonder if there is a way to get the calculated force into 
the pdo file or if it should be done manually (force=k*extension)?

/Malin Bergenstråhle

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