[gmx-users] Bonded parametrs for CG

[Elton Carvalho]

On Thu, Nov 22, 2012 at 12:27 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> Dear Gmx Users,
>
> What is the best way to extract bonded parameters from all atom
> simulation for the coarse grained model in gmx?

One posibility is starting with ad-hoc parameters, e.g. equilibrium
distances from the optmized AA structure converted to CG and ad-hoc
force constants, and tune them iteratively by comparing the bond
length, angle bend and dihedral distributions from the CG simulation
with an atomistic trajectory converted to CG.

--
Elton Carvalho
Tel.: +55 11 3091-6985/6922
Dept Física dos Materiais e Mecânica
Instituto de Física
Universidade de São Paulo
P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil