VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon May 25 2020 - 04:48:46 CDT

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
>