Multiwfn forum

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Generate electrostatic potential grid cube based on atomic charges

Today a CCL user asked a question:

Apologies if this is a naive question but I haven't had much success after finding solution
over internet. I want to generate electrostatic potential grid cube file using point charge
model for small molecules. Any suggestion for is highly appreciated. Thank you in advance.

Considering my reply may be useful for some Multiwfn users, I copy my reply here:

You can use Multiwfn (//www.umsyar.com/multiwfn) to easily generate electrostatic potential cube file based on atomic charge.

Below is an example of generating such cube file for water:

Write a plain text file named "water.chg" with below content
O -1.68940800 0.00002500 0.00194100 -0.728713
H -1.08142400 -0.01012400 -0.78063300 0.364427
H -1.06246900 0.00994900 0.76945700 0.364286
The 2,3,4 columns correspond to XYZ coordinates in Angstrom, and the last column corresponds to atomic charges.

Then boot up Multiwfn and input
water.chg
5 // Generate grid data
8 // ESP based on atomic charges
2 // Medium quality grid
Then you can use option -1 to visualize isosurface of the grid data, or use option 2 to export the grid data to .cub file.

Saran

Member

Registered: 2018-06-07

Posts: 5

Re: Generate electrostatic potential grid cube based on atomic charges

dear sir,

I tried to calculate the electrostatic potential surfaces of molecule by using multiwfn. package. but i could not succeed. the color is not changed which you have mentioned in the manual. here i have attached the image please check

i used the following manual. but i could not succeed.
Plotting electrostatic potential colored molecular surface map
with ESP surface extrema via Multiwfn and VMD

Last edited by Saran (2018-10-03 13:19:03)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Re: Generate electrostatic potential grid cube based on atomic charges

dear sir,

I tried to calculate the electrostatic potential surfaces of molecule by using multiwfn. package. but i could not succeed. the color is not changed which you have mentioned in the manual. here i have attached the image please check
https://i.postimg.cc/YjWrnHsF/fafa.png

i used the following manual. but i could not succeed.
Plotting electrostatic potential colored molecular surface map
with ESP surface extrema via Multiwfn and VMD

The most probable reason is that the color scale was not set properly, or coloring method was not properly chosen in VMD.
I strongly suggest you first reproduce the example given in my document to ensure that all your steps are correct.

Ihor

Member

Registered: 2018-10-05

Posts: 3

Re: Generate electrostatic potential grid cube based on atomic charges

Dear Sir,

I am a bit confused with units.
I tried 5 – 8 – 6 and successfully obtained ESP.
In output file we have 4 columns. First three (x,y,z) are in angstroms, but ESP is in atomic units.
Is this correct?

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Re: Generate electrostatic potential grid cube based on atomic charges

Dear Ihor,

I don't understand what does the 5-8-6 means.
The unit of exported data is always shown on screen, please carefully check the prompts, you will immediately know the unit used.

Ihor

Member

Registered: 2018-10-05

Posts: 3

Re: Generate electrostatic potential grid cube based on atomic charges

Dear Tian Lu,

Thanks for Your rapid response.
Unfortunately, I still can't find unit of exported ESP.

5 - 8 - 6 means followed sequence:
5 // Generate grid data
8 // ESP based on atomic charges
6 // Input center coordinate, number of points and extension distance

Then I input all grid data and generate ESP file.
However, as You may find in the attached picture (last line) unit of potential is still unknown.
Since all grid coordinates in the exported file are in angs., I am not sure, that ESP is exported in a.u.

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Re: Generate electrostatic potential grid cube based on atomic charges

Dear Ihor,

The unit of the calculated function is a.u.

Ihor

Member

Registered: 2018-10-05

Posts: 3

Re: Generate electrostatic potential grid cube based on atomic charges

Many thanks for the response

rikaaardoss

Member

Registered: 2020-07-29

Posts: 20

Re: Generate electrostatic potential grid cube based on atomic charges

Hello, I would like to take up again this post, since I made this same example, and the results I obtained were the expected ones, however, when trying to get the ESP from nuclear charges from a larger system, the results have unexpectedly high values between 50-80, initially I thought they were different units from a.u. but I feel there could be a relationship with the coordinates.

I appreciate the help in advance.

R.

N 79.179000 47.774000 -2.851000 7.000007
C 79.916000 46.524000 -2.868000 5.999965
C 78.948000 45.478000 -2.370000 6.000029
O 78.094000 45.778000 -1.550000 7.999992
C 81.122000 46.564000 -1.929000 5.999983
C 82.311000 47.397000 -2.380000 6.000051
C 83.191000 47.739000 -1.156000 5.999929
C 84.562000 48.310000 -1.531000 6.000038
N 85.307000 48.804000 -0.324000 7.000009
H 79.845000 48.521000 -2.986000 1.000000
H 78.647000 47.989000 -2.020000 1.000002
H 80.236000 46.289000 -3.883000 1.000008
H 80.799000 46.903000 -0.945000 1.000009
H 81.453000 45.545000 -1.727000 1.000004
H 82.898000 46.830000 -3.102000 0.999992
H 81.955000 48.319000 -2.840000 0.999993
H 82.665000 48.450000 -0.519000 1.000015
H 83.326000 46.846000 -0.546000 1.000013
H 85.151000 47.541000 -2.031000 0.999992
H 84.433000 49.130000 -2.238000 0.999991
H 85.447000 48.040000 0.322000 0.999998
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H 84.772000 49.532000 0.127000 0.999997
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H 78.421000 39.895000 -2.755000 1.000001
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C 76.497000 43.025000 0.944000 6.000004
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C 77.310000 46.673000 1.896000 5.999958
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H 73.225000 36.755000 -3.152000 1.000000
H 73.575000 35.600000 -0.956000 1.000000
H 75.231000 36.201000 -0.920000 1.000000
H 73.852000 38.537000 -1.372000 1.000000
H 72.662000 37.662000 -0.463000 1.000000
H 73.942000 37.810000 1.441000 1.000000
H 75.927000 38.851000 -1.331000 1.000000
H 77.182000 39.537000 -0.324000 1.000000
H 75.623000 38.725000 2.714000 1.000000
H 77.010000 39.465000 1.948000 1.000000

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,773

Website

Re: Generate electrostatic potential grid cube based on atomic charges

Hello, I would like to take up again this post, since I made this same example, and the results I obtained were the expected ones, however, when trying to get the ESP from nuclear charges from a larger system, the results have unexpectedly high values between 50-80, initially I thought they were different units from a.u. but I feel there could be a relationship with the coordinates.

The "high" result is expected. Because in your chg file, the last column is nuclear charges rather than atomic charges.