From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Nov 02 2006 - 17:22:45 CST
I'm sorry. This is the second e-mail I'm posting about this issue. Again a
question about what I read in the documentation:
> The center of mass of the SMD atoms will be harmonically constrained with
> force constant"k" (SMDk) to move with velocity "v" (SMDVel) in the
> direction "n" (SMDDir).
SMD thus results in the following potential being applied to the system:
U(r_1, r_2, ..., t) = 1/2 k [vt - (R(t) - R_0) . n ]^2.
What is the SYSTEM? Is it the whole protein or just the SMD atoms?
Thanks a lot,
Gianluca
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Dr. Gianluca Interlandi gianluca_at_u.washington.edu
+1 (206) 685 4435
+1 (206) 714 4303
http://biocroma.unizh.ch/gianluca/
Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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