SMD on center of mass

From: Gianluca Interlandi (
Date: Thu Nov 02 2006 - 15:40:40 CST

Can anybody tell me where in the code I can find the routine which
performs SMD (constant velocity pulling)?

In the documentation about SMD I read:

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).

How is this accomplished in the code? How is the force transfered to the
single SMD atoms?

I'm performing a simulation with two SMD atoms which are far apart from
each other, i.e. 15 A (I'm keeping another atom of the complex fixed).
Does this still make sense or do the SMD atoms need to be close to each
other in order for the SMD algorithm to work?

Any help on this would be appreciated.


Dr. Gianluca Interlandi
                    +1 (206) 685 4435
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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