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
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Jul 24 2012 - 02:00:03 PDT
