If what you want is the direct space contributions only, that is erfc(a *
r) / r, you can run mdgx in &debug mode. It may be possible to get this
information from sander with do_debugf engaged as well, but I am not sure.
What you'll need to do is take each frame as a starting condition and then
run a new calculation. This will print out the resulting forces and
energies due to the direct and reciprocal space components as MATLAB
scripts, which you can then read and pluck the energies from. However,
even these analyses may fall flat--there is not an N95 barrier between the
direct and reciprocal space components--rather, the 1/r contributions from
nearest neighbors must be removed as the reciprocal space component must
calculate everything, so if you want just erfc(a * r) / r for the
interacting pairs, with attenuations for 1:4 interactions, you've got a
problem akin to being given a three gallon and a five gallon jug, and asked
to come up with a sum of four gallons.
Another thing you might consider is setting dsum_tol to be ridiculously
close to 1, like 0.99999, such that all direct space interactions are going
to be truncated well before any two atoms can interact at all. Then,
you've got 100% reciprocal space energy, so you could subtract that from
the original imin=5 result for the standard calculation.
Dave
On Mon, Apr 6, 2020 at 4:10 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi!
>
> I am in need of a funky task for sander, do not ask why...
>
> We need to rescore (imin=5) a trajectory that was originally done using
> PBC/ewald.
>
> However, I need the energy using PBC but just the short range
> electrostatics, no the ewald reciprocal energy.
>
> Is there a way to do this ?
>
> adrian
>
>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Mon Apr 06 2020 - 14:00:02 PDT
