A good start might be:
Phys. Chem. Chem. Phys., 2011, 13, 10437–10448
This paper is about hybrid-models (mixing CG and AA). But they discuss
'boltzmann inversion' and 'force matching', which are both methods to
obtain CG-potentials.
Since they use small molecules it focusses on nonbonded interactions,
but one can probably transfer the methods to bonded interactions.
Greetings
Thomas
Am 26.11.2012 18:45, schrieb gmx-users-requ...@gromacs.org:
the distance distribution should be given by the Boltzmann factor of the
potential energy function between the beads, assigning V(r)=0 for the most
probable distance in your histogram. that's what you get when you take a
molecule in vacuum and for instance you compare the dihedral distribution
with the dihedral potential, the distribution is just exp[-U(theta)/RT],
except maybe for an additive constant.
you should be aware that the distribution may change appreciably depending
on the environment, so this approach may be tricky: you may include
implicit solvent effects on your bonded parameters and then you would end
up with a forcefield that counts twice the solvent effects on the internal
structure if you add explicit solvent in your model system.
I hope it helps.
Andre
On Mon, Nov 26, 2012 at 2:06 PM, Steven Neumann<s.neuman...@gmail.com>wrote:
>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,
>
>Steven
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