From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 13 2014 - 13:56:02 CDT
On Tue, May 13, 2014 at 2:34 PM, Michael Bellucci <bellucci_at_mit.edu> wrote:
>
> Dear NAMD users,
>
> I would like to know if there is a way to scale down solvent-solute
> intermolecular interactions while leaving the solute-solute and
> solvent-solvent intermolecular interactions the same? The closest thing I
> could find in the NAMD manual was the nonbonded scaling keyword, but this
> would scale down all intermolecular interactions. I also saw that NAMD is
> now capable of using tabulated potentials for specific pairwise
> interactions, but this seems to only be applicable to the VDW
> intermolecular interaction and not the coulomb interaction. Is there
> anyway to scale down solvent-solute intermolecular interactions without
> modifying the source code? Any help or suggestions would be appreciated!
>
how do you propose to handle long-range electrostatics for this? unlike
the short range coulomb term, this is not pairwise additive but rather a
manybody term and thus you cannot partition the interactions in the way you
want. basically, the amount of scaling would depend on the real space
cutoff, while normally it can be chosen rather freely to find the optimal
partitioning between the real space and reciprocal space coulomb force
calculation.
so you'd be forced to use cutoff-only interactions and then you could just
set all charges to zero and use tabulation. or use a different MD code
that has more flexibility (and typically correspondingly less performance).
axel.
>
> Mike
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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