[gmx-users] Umberella sampling

[chris.neale at utoronto.ca]

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

-- original message --

I can't understand correctly what we do when we are using umberella sampling
for obtaining PMF.
I explain that ,please modify or complete it.


(I think we define some sampling windows,each related to an reference
distance.
for each distance ,relative to it's distance,we define a spring constant.
our spring is at rest in the center of windows,
then we do a short simulation within each windows such that our molecule is
connected to the spring and it's potential energy is depending to it's
displacement from the center of windows.
Then we have potential energy of two molecules in any distance from each
other.
Having potential energy along the reaction path or here falong the degree of
freedom(distance between two molecules) is PMF oof interest and
the difference between limits of PMF plot is delta-free energy of interest)

what do you think ?do you agree with me?
Thanks in advance for your atteintion.
Mohsen