AMBER Archive (2009)

Subject: [AMBER] distance restraint and SHAKE

From: Michael J Yonkunas (myonkuna_at_andrew.cmu.edu)
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 2Å. 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,
M

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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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