I don't know all that is in the sander code, or perhaps even the pmemd
Fortran layer, but I can say that there is no support for fiddling with the
dielectric in the periodic GPU code, nor that I know of in the GB GPU
code. That said, if all you want is a change in the overall dielectric,
you can mimic this effect by scaling the charges in your simulation
topology and running igb=6 or periodic simulations with a fixed volume
(NVE, NVT, ntp=0). If you want a distance-dependent dielectric that's not
something any of the fast codes will support--as DAC said this is not
something we support because it is just not a preferred way of doing things
any more.
Dave
On Wed, Dec 30, 2020 at 11:44 AM Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> Hi David,
>
> Thanks for the response!
>
> An additional clarification- dielc=4 and eedmeth=5 would give a distance
> dielectric of 4r, but if I wanted a constant dielectric with some solvent
> box, would it instead be extdiel=4 with igb=6 instead? Or is there no
> modern equivalent to the constant dielectric (idiel=1) with a solvent box?
>
> Best,
>
> Kenneth
>
> On Sat, Dec 26, 2020 at 8:59 AM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Mon, Dec 21, 2020, Kenneth Huang wrote:
> > >
> > >The Amber5 manual mentions two dielectric functions (idiel=0 for
> distance,
> > >idiel=1 for constant) with the dielc controlling the constant.
> > >
> > >But I'm not clear on is how this would translate to amber16 sander? I
> > think
> > >if I want a gas phase with a dielectric of 4 I'd use
> > >
> > >#current min
> > >> &cntrl
> > >> ...
> > >> igb=0, extdiel=4,
> > >> ...
> > >> &end
> >
> > Above shouldn't work: extdiel is for GB calculations, but you have turned
> > GB
> > off. I think the combination you want is dielc=4 and eedmeth=5.
> >
> > Usual caveats: no developer has used this combination in a long time, and
> > we've removed it from the documentation. (It was already considered to
> > be effectively obsolete when the eedmeth variable was first introduced
> > 25 years ago.) So test carefully. And for sure, don't expect to get
> > physically reasonable results from this model.
> >
> > ....dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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Received on Wed Dec 30 2020 - 09:30:02 PST
