Re: Inspiration for most efficient implementation of coarse grained forcefield.

From: Jérôme Hénin (
Date: Mon Dec 15 2014 - 15:41:22 CST

Hi Ajasja,

My best guess is to have one atom type per CA and a lot of NBFIXes.


On 15 December 2014 at 19:08, Ajasja Ljubetič <>
> 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
> <
> >
> feature.
> 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)

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