AMBER Archive (2009)

Subject: [AMBER] distance restraint and SHAKE

From: Michael J Yonkunas (
Date: Tue Jan 27 2009 - 11:39:56 CST

Hello all,
I am running MD simulations of a patch of helices. I would like to keep these helices "helical" during some umbrella sampling calculations. I am currently using standard NMR restraints to hold the O-H atoms around 2. Although now that I think about this, it probably is not a good idea to use the SHAKE algorithm concurrently.

Anyone have any insight? SHAKE or no SHAKE? Better method of keeping helicity?

Much appreciated,

Michael J. Yonkunas
Molecular Biophysics
Dr. Maria Kurnikova Research Group
Department of Chemistry
Carnegie Mellon University
508 Mellon Institute
phone: (412)-268-1054

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