[gmx-users] Formula for cosine content in essential dynamics
spronk at umich.edu
Mon Aug 27 15:18:30 CEST 2007
Thank you, Berk, for clearing it up for me. I thought that maybe I didn't
understand something fundamental to the method. The formula lacking the 1/T
is in quite a few papers as well as the Gromacs manual. It has escaped
attention so far probably because g_analyze takes care of the calculation
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Berk Hess
Sent: Monday, August 27, 2007 9:11 AM
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Formula for cosine content in essential dynamics
>From: "Steve Spronk" <spronk at umich.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] Formula for cosine content in essential dynamics
>Date: Fri, 24 Aug 2007 17:04:04 -0400
>I am working on essential dynamics analysis of my protein, and I have a
>basic question on the calculation of the cosine content of the principal
>The way that I understand it, the first few principal components may
>resemble cosine functions, with the period equal to half the principal
>component index i. However, in the formula for cosine component listed in
>Hess's papers, the Gromacs manual, and all other sources I've checked, the
>cosine function is
>which is not actually a cosine that has a period of half the index. I must
>be misunderstanding something, because if you want to compare to a cos
>function that passes through half a period over the whole time of the
>simulation, shouldn't the formula include this instead:
>where T is the length of the simulation? This way, it also appears to me
>that the units work out correctly.
>I'm confused. Can you help me understand the formula better?
I probably forgot to add a factor of 1/T in the manual.
I'll fix it.
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