Unfolding simulations

From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Mon Jul 09 2007 - 01:18:26 CDT


Anyone have any experience with temperature dependent unfolding simulations
with NAMD? What kind of time steps and simulation times to use?
>From what I gather a 2fs time step @500K for about 8ns should be Ok for a
small protein (say something like ubiquitin). Any ideas?

Thanks in advance,


Arun Krishnan, Ph.D,
Assistant Professor,
Institute for Advanced Biosciences,
Keio University,
Center Building,
Tsuruoka, Yamagata 997-0035
Phone: +81 (0)235-29-0824
Email: krishnan_at_ttck.keio.ac.jp
URL: http://www.iab.keio.ac.jp/~krishnan

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