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

[Mao-Cai Yan]

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?
 
Thanks.
 
Stanley Yan
 
 
 
 
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