Re: SMD on center of mass

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

-----------------------------------------------------
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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