[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 00:51:56 CEST 2006

Mao-Cai Yan wrote:
> Hi dear friends,
> I just made an essential dynamics of 5ns; I calculated the cosine 
> content of PC1 by using
> g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg
> it gave: "Cosine content of set 1 with 0.5 periods: 0.749969"
> the value is rather too high.
> However, I found that only trajectory between 3300~3890 ps is useful, so 
> I calculated the cosine content during this period using
> g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 -e 3890
> and it gave: "Cosine content of set 1 with 0.5 periods: 0.297911"
> I want to know whether the essential dynamics is meaningful? The cosine 
> content of whole 5 ns is relative high, does it mean that the whole 
> trajectory is not meaningful? In another word, is it reasonable to use 
> "-b" and "-e" in the cosine content calculation?
What do you mean only a fraction is useful?
First check for equilibration (energy, rmsd etc.) then do the ED 
sampling after that, for a period that is considerably longer than the 
equilibration, e.g. an order of magnitude.

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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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