[gmx-users] Is 2D projection

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Fri Jul 7 09:33:41 CEST 2006

> Dear gmx users,
> Does the 2D projection plot has something to do with convergence of the
> trajectory? If so, what kind of shape of plot shows the trajectory is
> non-converged?
> Normally, I use RMSD plot to see if the trajectory tends to converge. Now
> my concern is how to see whether trajectory is conserved or not based on
> 2D projection analyses.
> Thanks in advance,
> Linda
you can, for example, have a look at the 2D projection of the trajectory 
onto the first two principal components obtained from the principal 
component analysis. In this paper Proteins 2005; 60:485 we used this kind 
of map to check the convergence of the simulation obtained from a replica 
exchange simulation with the counterpart obtained from high temperature, normal simulation.


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