[gmx-users] Bonded parametrs for CG

Elton Carvalho eltonfc at if.usp.br
Wed Nov 28 21:59:46 CET 2012

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

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