Hi all,
I am new to umbrella sampling and this is the first time I am doing this. I
have some questions
1) The shape of the biasing potential is more or less "U" shaped if we give
four different values for r1,r2,r3 and r4 but usually to approximate a
harmonic shape we give the same value to r2 and r3. Am I correct?
2) When we give distance restraints we usually write (atom#1 is fixed and I
am looking at the change in distance of atom#2 from atom#1)
&rst iat=1,2, r1=5, r2=10, r3=10, r4=15, rk2 = 32.83, rk3 = 32.83, /
In amber tutorial
http://ambermd.org/tutorials/advanced/tutorial4/ it says
that
"Conventionally, the violation energy is a well with a square bottom
between *r2* and *r3*, with parabolic sides out to a defined distance (*r1*
and *r4* for lower and upper bounds, respectively), and linear sides
beyond that distance"
Does the above mean that r1 is the distance to the left (towards zero) from
r2 and r4 is the distance to the right from r3 OR are all distances
measured from my reference atom (atom#1 in my case)?
I really appreciate your help.
Thank you
Sajeewa Dewage
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Received on Sun Nov 04 2012 - 21:00:02 PST
