[gmx-users] constraint force
kay.gottschalk at weizmann.ac.il
Sun Oct 3 12:37:49 CEST 2004
I have (again..) some questions about the constraint force.
a) What are the units? I couldn't really find it in the manual.
b) The manual states that a negative constraint force means attraction,
while a positive repulsion. Having in mind that there is an approach to
calculate the free energy profile by integrating the average constraint
force, this appears to be a problem. If you integrate the constraint
force as given by gromcas, you get a positive free energy when two
attracting particles approach each other. Am I getting this wrong?
c) How important is the choice of atoms I use to constrain the
distance? Does it make a difference to take just the CA as opposed to
the whole protein?
Since there is some discussion in the literature about when (if) it is
appropriate at all to get a free energy profile by integrating the
average constraint force, I would be grateful for some opinions on this
Thanks a lot!
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