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

M. Yan yanmaocai at 126.com
Mon Sep 11 03:40:40 CEST 2006

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? 

-----Original Message-----
From:"David van der Spoel" 
Sent:2006-09-11 09:20:33
To:"M. Yan" 
Title :Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC?

M. Yan wrote:
> Hi,
> In fact I simulated 30 nanoseconds, but I found the system reached 
> equilibrium at 4.4 ns (by analyzing RMSD, Energy and visualizing, 
> etc.) and did not change significantly in the last 25 ns. Thus I want to 
> do an essential dynamics for the first 5 ns.
> I also calculated the covariance matrix for the whole 30 nanoseconds, 
> but the cosine content of PC1 is still as high as 0.710. However, MD 
> simulation longer than 30 ns is beyond our compute ability. Then what 
> shall I do?
> Thanks.
Try ED of the last 25 ns only. The first 5 represent equilibration and 
unless you are specifically interested in th force field issues etc. 
related to that, you should discard those 5 ns for analysis.

Then try to do other analyses as well and try to make sense of the whole 
simulation. IIRC the cosine content being high indicates that the 
protein performs a random walk on a relatively flat free energy surface. 
This is informative in itself but needs to be considered in the context 
of additional analysis and the background of your investigation.
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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