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.
Phuong
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