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

[M. Yan]

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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060911/13e1d2e8/attachment.html>