tcl forces/membranes

From: David A. Horita (
Date: Tue Dec 09 2008 - 15:28:07 CST

How do I write a constant-velocity script using tcl forces? I realize
this was covered a few years ago in this group, but the attached script
didn't make it into the archive.
Basically, I'm trying to pull a membrane-binding protein off a membrane,
but when using SMD the membrane moves along with the protein (eventually
it falls off, but this really messes with the force analysis). I was
thinking of using SMD to constrain the membrane to zero velocity and TCL
forces to pull the protein. If anyone has a better way of doing this,
I'd be interested (possibly using SMD for the protein and TclBC for the
membrane?). I can do this with namd constraints for specific membrane
atoms, but I was hoping for something a bit more
gentle/center-of-mass-related, especially after spending a bunch of time
to equilibrate the membrane.
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671

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