[gmx-users] Re: how is the pulling force measured

kim2811 kmanibog at iastate.edu
Tue Apr 30 08:38:36 CEST 2013

Hi Alex,

I read the manual but I got confused with the details. My pull_geometry =
position with pulling direction along y. I am trying to dissociate two
interacting proteins. So I set the last amino acid of one protein as my
reference group and the last amino acid of the other protein as the pulled
group. Now, I don't know exactly how to interpret what reference group and
pulled group mean, and what is their difference; since in the manual it says
'there is no difference in treatment of the reference and pulled group
(except with the cylinder geometry).' Also, it says that measured force
output is the force of the pulled group. 

So basically, I am trying to visualize how the system works. Using the
pull_geometry stated above, are the two groups (reference and pulled)
attached to two virtual springs? Will this statement be correct?

"Force was applied by moving the clamped ends of the two springs (i = 1, 2)
in opposite directions with constant velocity v to positions Zi(t) = zi(0) +
vt, where zi(0) is the initial position of the end of the molecule. The
forces fi(t) at the two ends were measured at every time step using the
relationship fi(t) = k (zi(t) − Zi(t))."   

I hope my questions make sense. Thank you.

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