[gmx-users] Bonds - force constant for given Beads

Steven Neumann s.neumann08 at gmail.com
Mon Nov 26 17:06:14 CET 2012

Dear Gmx Users,

I am planning to build coarse grained model based on the all atom
simulation. I created (using VMD) beads representing 2-4 atoms of my
protein chain. I want to extract bonded parameters. The equilibrium
lenght for bonds (between specified beads) would be the average over
the equilibrium from all atom simulation using g_dist between Centre
of Mass of group of atoms belonging to given bead.

My question: How can I extract the force constant for the bonds from
all atom simulation between those beads?

Thank you,


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