VMD-L Mailing List

From: Sebastian Reiter (Sebastian.Reiter_at_campus.lmu.de)
Date: Mon May 25 2020 - 04:10:18 CDT

Hi Francesco,

the electrostatic potential is usually mapped onto the electron density
but it sounds like you are plotting the potential directly.

You could try creating one cube for the density, one for the potential
and loading both into the same molecule. Then you can plot the density
in the Isosurface representation and color it by Volume, where the
volume comes from the potential cube file. You may also have to adjust
the color scale in the Trajectory tab.

Best
Sebastian

Am 25.05.20 um 10:03 schrieb Francesco Pietra:
> I had already tried that. I was able to raise the isosurface but unable to
> color it by charge. Color by ID provides a single color for the whole
> surface.
>
> I also tried a proven cube file for water, coming from GAUSSIAN itself:
> same issue.
>
> Are those really surfaces and not volumes?
>
> francesco
>
> On Sun, May 24, 2020 at 11:32 PM Mortimer Hemmit <mortimer.hemmit_at_gmail.com>
> wrote:
>
>> If you want to load the cube into VMD using the file reader, I think
>> it is already inside VMD. Try to load a new molecule and there is a
>> "Gaussian Cube" file type.
>>
>> Mortimer
>>
>> On Sun, May 24, 2020 at 10:31 AM Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>> As to my previous request of a tool devised to treat electrostatic
>> potential maps, I have now found an obsolete "readcube.tcl" by
>> Gervasio/Stone.
>>> As I am unable to color by charge the surface with this tool, from where
>> can "Gaussian cube file reader" mentioned among "Volumetric Data/Density
>> Potential Map Plugins" (
>> https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/)? I would like to
>> install on VMD it and try.
>>> thanks
>>> francesco pietra
>>>
>>> ---------- Forwarded message ---------
>>> From: Francesco Pietra <chiendarret_at_gmail.com>
>>> Date: Sat, May 23, 2020 at 10:20 AM
>>> Subject: Electrostatic potential maps
>>> To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>>>
>>>
>>> Hi all
>>> I am looking for a general script for electrostatic potential maps from
>> cube files produced by the python script mep.py from ORCA data.
>>> thanks
>>> francesco pietra