[gmx-users] What is an acceptable cosine content values?

[Tsjerk Wassenaar]

Hi Catherine,

> When we use cosine content to determine if our simulation are converged or
> not, should I

You can't use the cosine content to determine if a simulation is
converged. You can only use it to determine whether the simulation is
not converged, which is quite a different thing.

> (1) sum all the first three principal components together or examine
> individually?

Determination of the cosine content is done by means of fitting, and
the cosine content can be regarded a correlation coefficient, which is
one for a perfect fit and 0 for no fit. That only makes sense for one
pc. The analysis is thus performed per component.

> (2) If I expect the first 10 ns is the equilbrium period, while the other 20
> ns as the production period.  Should I include all 30 ns of trajectory to
> the analysis or should I just include the last 20 ns trajectory to the
> analysis?

No, you should perform the analysis on the part you intend to use for
all analysis.

> (3) Let's if I got the PC1 as low as 0.3, can I still claim the trajectories
> are converged?

No. You can claim that the cosine content is low, but that is not the
same as being converged.

> (4) Did you comes across that when you increase the simulation time, the
> cosine content values of the first three principal components did not goes
> down but increased?

May very well happen. Especially if the system tips over to a
previously unexplored region of conformational space due to a
conformational change or internal rearrangement.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands