analysis of simulation output

From: James Starlight (
Date: Thu Jun 27 2013 - 13:25:38 CDT

Dear NAMD users!

I wounder to consider possible options for the simulation analysis. In
particular besides some common options (like RMSD, RMSF etc) I wounder to
analysis dynamics of the non-polar contacts (intermolecular salt-bridges as
well as hydrogen bonds between protein and diffusional ligand) along the
trajectory. I'll be thankfull for any usable tutorial.

Thanks for help,


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