Umbrella sampling
Dear all,
I am new to umbrella sampling and i am bit confused about the procedure and
i would be glad if you can clear my doubts.
I want to use umbrella sampling to checkthe free energy profile during
conformational change of protein along a particular reaction coordinate .
(for example distance between two atoms )
As i understand we run a series smaller simulations such that the restart
file (.rst) generated at the end of one simulation (window1 ) is used as
input (starting structure) for the next simulation ( window 2) and then the
result is used for WHAM analysis. Naturally this becomes very tedious ;) .
or do we run independent simulations (using different restraint file-
varying the values of r1, r2, r3, and r4 ) using same starting structure
(.crd file) as described in Dr.Tings tutorial ? (
http://projects.eml.org/mcm/people/wang/PMF/tutorial.html) .But then i need
to have different restraint files.If i want to hthe distance to be around
14A can i start with r2=r3=0 (on what basis do we vary the values of r2 and
r3 - is there a particular range ) .
# distance restraint
&rst iat=1402,4276, r1=-100.0, r2=14.0, r3=14.0, r4=100.0, rk2 = 30.0, rk3
= 30.0, /
how do i do it ?
Thanks for the suggestion
sid
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Received on Mon Apr 04 2011 - 09:00:03 PDT
