Jan-Philip,
I think Wes meant to say the energy is in kcal/mol, so potential would be
kcal/mol-e ... This is how things work within Amber. "e" is the atomic unit
of charge. It is always positive, i.e. the electron charge is -e, the
proton charge is +e.
Hope this helps.
Ray
On Tue, Jul 24, 2012 at 1:55 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Dear Wes,
>
> thanks for the quick response. Just to be sure, do we both agree that
> the potential must have the unit energy per charge, as opposed to your
> comment "The original intent was to use kcal/mol"? I.e. the unit should
> be kcal/(mol*e). We should also agree on e>0 in this case, so that a
> positive potential value means repulsion of a positive charge.
>
> Thanks,
>
> Jan-Philip
>
> PS: what is the status about this missing-newline-in-DX-file-bug? Will
> you release an official patch based on the I changes I proposed?
>
>
>
> On 07/23/2012 10:34 PM, wmsmith.uci.edu wrote:
> > I just checked through the code for the appropriate line in pb_force.F90.
> > Using the DX format (phiform=2), it appears that it is just printing out
> > the raw array data. This seems to be rather strange units. The original
> > intent was to use kcal/mol (same as with phiform=1), so I will submit a
> > bugfix patch. As Dr. Luo mentioned, force would then be in kcal/mol-e-A
> if
> > calculated from the corresponding grid.
> > -Wes
> >
> >> Since Amber uses kcal/mol for energy, kcal/mol-A(ngstrom) for force, so
> >> the
> >> potential unit is kcal/mol-e and the field unit is kcal/mol-e-A. Wes may
> >> want to clarify on this as well.
> >>
> >> Ray
> >>
> >> ---------- Forwarded message ----------
> >> From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
> >> Date: Mon, Jul 23, 2012 at 8:43 AM
> >> Subject: [AMBER] pbsa: unit of the electrostatic potential values
> written
> >> to DX file
> >> To: AMBER Mailing List <amber.ambermd.org>
> >>
> >>
> >> Dear PBSA developers,
> >>
> >> what is the unit of the electrostatic potential values written to a DX
> >> file by pbsa? Is this documented somewhere?
> >>
> >> Thanks,
> >>
> >> Jan-Philip
> >>
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
>
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Received on Tue Jul 24 2012 - 11:30:03 PDT
