[gmx-users] Re: Bonds - force constant for given Beads
schlesi at uni-mainz.de
Mon Nov 26 20:23:58 CET 2012
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
Since they use small molecules it focusses on nonbonded interactions,
but one can probably transfer the methods to bonded interactions.
Am 26.11.2012 18:45, schrieb gmx-users-request at 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.
> 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,
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