[gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC?

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 11 04:31:34 CEST 2006

M. Yan wrote:
> Thank you very much.
> The significant conformation changes occurred between 3.3ns and 3.9ns, 
> which I am interested for. The cosine content in this 0.6ns is low (just 
> 0.29; calculated by "g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 
> -e 3890"); I want to know whether it indicates that the movement of 
> protein IN THIS 0.6ns is believable?
That depends, since you only see a single event in your 30 ns. It would 
be more convincing if you could show that this is reproducible, by doing 
multiple simulations with different conditions (e.g. velocities, 
temperature, starting structure). If it then happens early on in the 
simulations, and they all converge to the same structure as your 30 ns 
simulation, then it would be convincing...

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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