[gmx-users] Bond potential of atom groups

[Steven Neumann]

I have VOTCa already installed. Thank you for this.

Steven

On Wed, Feb 13, 2013 at 10:34 PM, Broadbent, Richard
<richard.broadbent09 at imperial.ac.uk> wrote:
> 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.
>
> Regards,
>
> Richard
>
> 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
>>
>>Steven
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