VMD-L Mailing List

From: Sebastian Reiter (Sebastian.Reiter_at_campus.lmu.de)
Date: Mon May 25 2020 - 06:35:18 CDT

Hi Francesco,

1) The orca_plot program also has an option to plot the full SCF
density, not just individual orbitals.
2) You can first load the density file and then load the potential into
the same molecule (select the ID of the first cube file in the molecule
file browser instead of "New Molecule"). In the end, you should see one
molecule ID with two volumetric data sets in VMD.
3) orca_vpot uses the electron density to compute the potential at
certain points in space. To visualize this potential, you typically plot
the density as an isosurface and map the potential as a color onto that
surface, so you still need a cube file for the density.

In total, the following process has worked for me:

1. Run Orca with the keyword "KeepDens". This generates a file with the
extension .scfp that contains the density.
2. Run the command "orca_plot filename.gbw -i" and in the interactive
menu select the following options to generate a cube file for the density:
        * Enter type of plot -> electron density
        * Select output file format -> Gaussian cube
        * Generate the plot
3. Run the mep.py script (https://gist.github.com/mretegan/5501553) to
generate a volumetric cube file for the electrostatic potential.
4. Load both cube files into vmd, either with the molecule file browser
(see above) or with the -f command line option:
        vmd -f filename.eldens.cube filename_mep.cube
5. Create an Isosurface representation for the density, color by Volume
and select the potential cube file as the data set for the color.
6. Adjust the color range in the Trajectory tab of the Representations
window.

Best
Sebastian

Am 25.05.20 um 11:48 schrieb Francesco Pietra:
> also, as far as I can understand, orca_vpot already takes into account the
> electron density from the .gbw file
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, May 25, 2020 at 11:41 AM
> Subject: Re: vmd-l: Fwd: Electrostatic potential maps
> To: Sebastian Reiter <Sebastian.Reiter_at_campus.lmu.de>
> Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> Hi Sebastian
> I have two problems following your suggestions
>
> 1) "You could try creating one cube for the density, one for the
> potential":
> ORCA, for the electron density requires specifying for which orbital,
> while
> "*orca_vpot* filename.gbw filename.scfp filename.vpot.xyz
> filename.vpot.out"
> for the electrostatic potential does not.
>
> 2) "and loading both into the same molecule"
> what do you mean for "same molecule"? the xyz file?
> I am used to load into a .psf, while here I am confused.
>
> Other visualization software plot the electrostatic potential directly onto
> the surface, not the volume.
>
> thanks
> francesco
>
> On Mon, May 25, 2020 at 11:10 AM Sebastian Reiter <
> Sebastian.Reiter_at_campus.lmu.de> wrote:
>
>> 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