On 2/21/13 6:24 PM, Yun Shi wrote:
So in umbrella sampling, does it really matter if the vector
connecting the COMs of protein and ligand is NOT parallel with the
vector of the pulling force (although the pull rate is 0)?
I guess as long as the force in each sampling window is along the same
direction, we can in theory get potential of mean force along any
direction.
I honestly don't know how that would affect things. Perhaps someone else who
has dealt with such cases can comment, but typically it is easiest to define the
reaction coordinate to be coincident with the direction(s) along which you wish
to apply the umbrella restraint.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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