Re: Unfolding simulations

From: Neema Salimi (nsalimi_at_msg.ucsf.edu)
Date: Mon Jul 09 2007 - 12:17:08 CDT

2fs may be a little long. I had much better energy conservation
(NVE) at high temps with a 1 fs timestep. Ubiquitin will easily
unfold in 8 ns at 500K. I'm of the opinion that 500K may be a bit
much temperature-wise for some of these little proteins, but others
will surely disagree.

On Jul 8, 2007, at 11:18 PM, Arun Krishnan wrote:

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

Neema Salimi
nsalimi_at_msg.ucsf.edu

University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
http://msg.ucsf.edu/agard/
Lab Phone: (415) 476-5143

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:36 CST