RE: NAMD-L: question about harmonic constraints

From: JC Gumbart (
Date: Sat Apr 08 2006 - 13:52:02 CDT

It is possible to use SMD with a velocity of zero to restrain the center of
mass of atoms along one axis. However, if you try to restrain along more
than one axis, very interesting problems will arise.

Unfortunately, for anything more, I believe scripting with tclForces may be
the only option.

-----Original Message-----
From: [] On Behalf
Of Margaret Shun Cheung
Sent: Saturday, April 08, 2006 1:34 PM
Subject: namd-l: NAMD-L: question about harmonic constraints

Dear NAMD users,

I looked up the user guide for harmonic constraints and the option is that
each assigned atom is referenced to a specific coordinate in the
"consref <file>". What should I do if I want to impose harmonic
constraints to
the center of mass of several atoms during the simulations instead (like
what SMD does to the selected SMD atoms)? I looked up selectcontrX{Y,Z}
too, but probably it's not what I was thinking for.

Please share me with your insights!
Thank you very much!
Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,

Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland
College Park, MD 20742-2431 email:

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