[gmx-users] Bond potential of atom groups

Broadbent, Richard richard.broadbent09 at imperial.ac.uk
Wed Feb 13 23:34:33 CET 2013

Dear Steven,

There is no universal method to do this and many people spend years
studying the various techniques. However,
http://pubs.acs.org/doi/abs/10.1021/ct900369w gives an overview of some of
the most widespread techniques used and its references will provide
further details. Futhermore, the VOTCA code it describes (www.votca.org)
provides tools for building such potentials and is compatible with gromacs
file formats.



On 13/02/2013 16:07, "Steven Neumann" <s.neumann08 at gmail.com> wrote:

>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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