[gmx-users] cosine content and nonconverged trajectory

[Justin Lemkul]

On 11/2/12 8:17 AM, ahmet yıldırım wrote:
> Dear users,
>
> The cosine content of the principal components is an effective
> indicator for predicting whether or not a trajectory has been
> convergent. A high cosine content typically indicates a nonconverged
> trajectory (Chapter 5: Normal Modes and Essential Dynamics Steven
> Hayward and Bert L. de Groot).
> What is a high cosine content? 0.2, 0.5 or 0.7 What is the value?
>

There have been numerous discussions on this topic in the past.  A few that come 
to mind immediately are in the following threads:

http://lists.gromacs.org/pipermail/gmx-users/2011-December/066921.html
http://lists.gromacs.org/pipermail/gmx-users/2012-April/070374.html

Check the list archive for more.

-Justin

> Thanks in advance
> --
> Ahmet Yıldırım
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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