[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 03:20:43 CEST 2006

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?

Original message:"David van der Spoel" 
Sent:2006-09-11 06:51:56
To: "Discussion list for GROMACS users" 
Object:Re: [gmx-users] May I use "-b" and "-e" in the cosine con tent calculation of PC?

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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