Re: Analysis plugins for Martini Coarse Grained protein simulations

From: Fotis Baltoumas (
Date: Sat Feb 07 2015 - 05:25:50 CST


There's the Bendix plugin for Coarse Grain result analysis (under the
visualization sub menu). This can help you for visualization and secondary
structure work. As for RMSD and Radius of gyration, you can simply use
the already existent RMSD tools and tcl interface in VMD. Just replace
your typical all atom selections with the appropriate coarse grained ones
(for example, instead of "name CA" or "backbone", use "name BAS" for CG
backbone RMSD calculations in the RMSD trajectory analyzer).

Hope I helped,

Fotis Baltoumas

> Dear All,
> I have been working on simulating a protein aggregation related problem
> using the residue based coarse graining approach using the MARTINI
> forcefield. I want to know if there are any post-processing analysis
> scripts/plugins available for the coarse grained trajectories like for the
> all atom trajectories.
> Please let me know if there are any already available for secondary
> structure assessment via dihedral angles, RMSD, Rg etc.
> Thanks and Regards
> Srivastav R

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