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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists