Hi all and Jason,
I need the external electrostatic potential acting on a subset of atoms
from PME. Is it clearer this way?
Sorry for the long preface :)
Elisa
On Tue, Jul 5, 2016 at 8:17 PM, Jason Swails <jason.swails.gmail.com> wrote:
> I'm not quite clear what you're wanting. I can think of 2 things:
>
> 1. The ESP from each non-QM atom in the system on the QM atoms so you can
> provide that as input to Gaussian?
>
> If this is the case, you can just add point-charges to the Gaussian input
> file directly that correspond to each atom outside the QM region instead
> and Gaussian will do that for you.
>
> 2. The ESP on each atom from the combined QM/MM Hamiltonian?
>
> I think you can just use the Gaussian cube file that you can generate from
> the QM calculation to compute this directly from the resulting
> wavefunction/electron density. (I did it a long time ago, and can't
> remember all of the details).
>
> HTH,
> Jason
>
> On Tue, Jul 5, 2016 at 12:20 PM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
>
> > Yes, sorry, I took it for granted. I'm talking about electrostatic
> > potential!
> >
> > Elisa
> > Il 04/lug/2016 18:23, "Adrian Roitberg" <roitberg.ufl.edu> ha scritto:
> >
> > > Hi Elisa
> > >
> > > Can you clarify what you mean by 'potential on each atom' means?
> > >
> > > You can take a snapshot from amber, convert those coordinates to a
> > > format gaussian understand and compute whatever you want with gaussian
> > > itself. Not sure what you mean by the 'potential' here.
> > >
> > > adrian
> > >
> > >
> > >
> > > On 7/4/16 10:43 AM, Elisa Pieri wrote:
> > > > Dear all,
> > > >
> > > > I'm taking snapshots of a peptide from an Amber trajectory, I need to
> > > > perform energy calculations on each geometry using Gaussian. In order
> > to
> > > > proceed in my calculations, I need to know the potential on each atom
> > of
> > > my
> > > > peptide. How can I get this information?
> > > >
> > > > Elisa
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > --
> > > Dr. Adrian E. Roitberg
> > > University of Florida Research Foundation Professor.
> > > Department of Chemistry
> > > University of Florida
> > > roitberg.ufl.edu
> > > 352-392-6972
> > >
> > >
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> > >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
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>
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Received on Wed Jul 06 2016 - 07:30:02 PDT
