[gmx-users] Analysis and visualization of CG trajectories

[James Starlight]

Dear Gromacs users!

I wonder to ask someone who already performed MARTINI simulations of
membrane proteins regarding visual and statistical methods for the
analysis of that simulations. Particularly what is expecially
interesting for me is i) visualization of protein-protein interactions
in CG models- I have tried bendix plugin implemented in VMD but found
it not very confortable; ii) analysis of conformational changes within
each monomer assuming that I dont use any elastic restrains during my
CG runs- e.g will the PCA works there assuming that I will use 1
martini node for calculation of cov-matrix instead of C-alpha atom
used in case of the PCA of full-atomic trajectory; iii) any of the
clusterization methods e.g to discriminate between different contact
areas of monomers during md run.

Thanks for help in advance!

J.