[gmx-users] Bond potential of atom groups

Steven Neumann s.neumann08 at gmail.com
Wed Feb 13 17:07:53 CET 2013

Dear Gmx Users,

I want to create coarse grained model. I need bond constant and
equilibrium distance according to the equation

V(r) =K (R - Req)^2

I wish to extract bonded potential between beads made out 3 atoms. I
need Req and K. Equilibrium distance is straight forward - g_dist
between COM or COG with index file conatining those 3 atoms. To match
force constant K  I need to extract bonded potential and try to fit to
my parabolic curve.

My question:

How can I get bonded potential between beads of 3 atoms from AA
simulation? Do I have to specify energy groups (energgrps) before the
run in my mdp and then use g_energy?

Thank you


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