Inspiration for most efficient implementation of coarse grained forcefield.

From: Ajasja Ljubetič (
Date: Mon Dec 15 2014 - 12:08:03 CST

Dear all,

I would like to run coarse grained simulations of protein folding similar
to Chavez et. al. <> (here is
the supplement
The model is meant to study entropic barriers to protein folding (and is
capable of predicting folding rates if the experimental melting temperature
is known),

Basically this involves taking only the C-alpha atoms from a known
reference structure and determining the equilibrium values for bonds,
angles and dihedral angles from the reference. Then a vdw-like potential is
applied, that is specific for different atom pairs. Atoms that are close
together get an attractive+repulsive part, all other pairs get only the
repulsive part.
[image: Inline images 1]

My first thought was to have a single atom type and account for all the
different bonds and angles using NAMD's extraBonds
But I don't see a way to have per atom pair specific vdw forces. So my
first question is: *is there a way to have per-atom pair specific
attractive/repulsive nonbonded potential? *(without resorting to TCLforces)--001a1137cf72ad4bd8050a451fc9--

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