[gmx-users] Calculation Population densities on the PCA projections

[James Starlight]

Dear Gromacs Users!

My question is about Essential Dynamics Analysis emplemented in
GROMACs (projections of the MD trajectory onto some Principal
components extracted from that runs) . In particular I wounder to know
is there any way to measure population density ( or free energy
levels) for the MD conformers projected onto some principal
components. In other words I'd like to know in what parts of
conformational space my protein have been mostly populated during MD
simulation.

Some example of such analysis can be found in the paper below where
the dynamics of the membrane receptors have been investigated.
http://pubs.acs.org/doi/abs/10.1021/ja205313h

In that case the free energy diagrams have been calculated from the MC
sampling which was done before MD run. On other hand I'd like to know
if is't possible to calculate energies from EDA (covariance matrix
decomposition for instance )?


Thanks for help,

James