Dear Christoph,
Thank you very much for your advice.
Do you mean that if I use csg_inverse and then the obtained distributions
for both bond and nonboned interactions fit to target distributions, the
potentials are already extrapolated and ready to be used?
If the simulation runs with those potentials, are the roughed forces fine?
Thank you.
Best regards,
Changwoon Jang
On Wed, Feb 3, 2016 at 4:41 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-02-03 13:40 GMT-07:00 Chang Woon Jang <[email protected]>:
> > Dear Votca Users,
> >
> > I am wondering about extrapolating non-bonded and bonded (bond and
> > angle) potentials from csg_inverse.
> >
> > For the bonded and non-bonded potentials obtained from Iterative
> > Boltzmann Inversion, they do not have poorly-sampled regions in
> > table_XXX.xvg files. Those non bonded potentials and forces are smooth
> and
> > look similar to Lennard Jones potential curve. Those bonded potential are
> > also smooth and U shapes. But the forces are look ugly in the side of the
> > minimum.
> To clarify the *.xvg are the extrapolated and smoothed version of the
> potentials.
> For the rough version, have look at *.pot.new
>
> >
> > Questions?
> >
> > 1. If there are no poorly-sampled regions in both bonded and non-bonded
> > potentials from csg_inverse, can I just use those potentials for CG
> > simulations?
> Yes! An iteration step is already a short CG simulation.
>
> >
> > 2. Do I need to resample and extrapolate bonded FORCES if those have
> > poorly-sampled regions?
> You can always fit the potential with a smooth function or increase
> the step value to make potentials and hence forces smoother, but as in
> 1.) if it runs you should be fine.
>
> Christoph
>
> >
> > Thank you very much for your advice.
> >
> > Best regards,
> > Changwoon Jang,
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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