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

[André Farias de Moura]

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.neumann08 at 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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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090