Since your system is too complex, I suggest you first using VASP to calculate a simple system such as a water molecule to check whether the ESP over the vdW surface can be normally produced via the aforementioned way.
]]>Hartree potential is different to ESP, it only corresponds to the electrostatic potential due to electron density. In contrast, in the definiton of ESP, the nuclear charge contribution is also taken into account.
So you think I should use the Total electrostatic potential, which also include the XC part ? Because vasp already include the ionic+Hartree in the output file.
]]>Thank you very much for your reply. I am sure there is no problem of charge and potential. CHG.cube is the charge density and POT.cube is the Local Hartree potential from LOCPOT output file. I think the abnormal may comes from the mismatch of VASP and Multiwfn. I will check more carefully.
Thank you again for your suggestion and patience
Dear Lu
I followed your suggestion and check each item for installing multiwfn and it remained the same.
So, I find a new computer with win10 and tried the multiwfn_3.7_dev. And the program collapsed at
0 // Start calculation
ESP.cub // The cube file recording ESP
I do not know what the problem. Can you check what happens?
I updated Multiwfn today, this version is able to normally perform quantitative molecular surface analysis based on your cube file, the resulting map is shown below
If the grid data contained in the POT.cub is ESP, the map seems to be weird. Since I am familiar with VASP, I cannot give you more advice.
]]>I followed your suggestion and check each item for installing multiwfn and it remained the same.
So, I find a new computer with win10 and tried the multiwfn_3.7_dev. And the program collapsed at
0 // Start calculation
ESP.cub // The cube file recording ESP
I do not know what the problem. Can you check what happens?]]>
This problem of Linux version commonly implies that the Multiwfn has not been installed properly, please carefully follow the installation steps in Section 2.1.2 of Multiwfn maual.]]>
Here is the output information
Differential element: 0.0021970507 Bohr^3
Summing up positive value in grid file: 1141005.3814225656
After multiplied by differential element: 2506.8466724032
Summing up negative value in grid file: -1141005.3785599838
After multiplied by differential element: -2506.8466661140
Summing up all value in grid file: 0.0028625818
After multiplied by differential element: 0.0000062892
Loaded POT.cube successfully!
^Cforrtl: error (69): process interrupted (SIGINT)
Image PC Routine Line Source
Multiwfn 0000000001AF4D64 Unknown Unknown Unknown
libpthread-2.17.s 00002B10BA0C05F0 Unknown Unknown Unknown
libc-2.17.so 00002B10BA3C0BED __poll Unknown Unknown
libxcb.so.1.1.0 00002B10BBBB305A Unknown Unknown Unknown
libxcb.so.1.1.0 00002B10BBBB0E43 xcb_connect_to_fd Unknown Unknown
libxcb.so.1.1.0 00002B10BBBB4A73 xcb_connect_to_di Unknown Unknown
libX11.so.6.3.0 00002B10B9826F0A _XConnectXCB Unknown Unknown
libX11.so.6.3.0 00002B10B9817D92 XOpenDisplay Unknown Unknown
Multiwfn 0000000000B81EAC Unknown Unknown Unknown
Multiwfn 0000000000B9F634 Unknown Unknown Unknown
Multiwfn 00000000007934FB Unknown Unknown Unknown
Multiwfn 0000000000430922 Unknown Unknown Unknown
libc-2.17.so 00002B10BA2EF505 __libc_start_main Unknown Unknown
Multiwfn 0000000000430829 Unknown Unknown Unknown
Input file path, for example E:\iDOLM@STER\Makoto_Kikuchi.wfn
(Supported: .mwfn/wfn/wfx/fch/molden/31/chg/pdb/xyz/mol/mol2/cub/grd, etc.)
Hint: Press ENTER button directly can select file in a GUI window. To reload t
e file last time used, simply input the letter "o". Input such as ?miku.fch can
open the miku.fch in the same folder as the file last time used.
H:\POT.cube
Please wait...
Title line of this file:
CUBE FILE CONVERTED FROM VASP format
OUTTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
Total number of atoms: 196
Translation vector: X Y Z (Bohr)
Vector 1: 0.130001 0.000000 0.000000
Vector 2: 0.000000 0.130001 0.000000
Vector 3: 0.000000 0.000000 0.130001
The range of x is from 0.000000 to 27.950215 Bohr, 216 points
The range of y is from 0.000000 to 27.950215 Bohr, 216 points
The range of z is from 0.000000 to 27.950215 Bohr, 216 points
Total number of grid points: 10077696
This grid data will take up at least 76 MB memory
Loading grid data, please wait...
The minimum value: -0.41183300E+01 at 3.640028 19.890153 21.190163 Bohr
The maximum value: 0.22817000E+00 at 16.380126 0.390003 26.650205 Bohr
Differential element: 0.0021970507 Bohr^3
Summing up positive value in grid file: 1141005.3814225656
After multiplied by differential element: 2506.8466724032
Summing up negative value in grid file: -1141005.3785599838
After multiplied by differential element: -2506.8466661140
Summing up all value in grid file: 0.0028625818
After multiplied by differential element: 0.0000062892
Loaded H:\POT.cube successfully!
Formula: H28 Li7 C56 N7 O42 F42 S14
Molecule weight: 2766.27302
Point group: C1Then the main function menu is shown, you can use proper options to start analysis.
]]>Thank for your reply and suggestions.
I tried as your suggestion with Multiwfn 3.7, But it remained the same. Here are the files of CHG.cube and POT.cube
https://pan.baidu.com/s/1QgmZluAKMfeg2vD1duVzWg ysdk]]>
Hi
I also tried this method by generation charge density and potential cube file from VASP calculation by files format conversion. And when I followed your suggestion and Multiwfn just stopped at: Loaded CHG.cube successfully! I used the Multiwfn version 3.6 and The cell in my calculation is cubic cell. I also checked the CHG.cube and POT.cube by Vesta and they all show normally. I do not know what happens and can you give me some tips?
I didn't test compatibility with cube file of VASP. Since some codes related to grid data reading has been changed during development of Multiwfn 3.7(dev), I suggest you try 3.7(dev) first, if the latest version is still unable to load your cube file, please upload the cube file to a netdisk and show me link, I will download and try to figure out the reason.
]]>I also tried this method by generation charge density and potential cube file from VASP calculation by files format conversion. And when I followed your suggestion and Multiwfn just stopped at: Loaded CHG.cube successfully! I used the Multiwfn version 3.6 and The cell in my calculation is cubic cell. I also checked the CHG.cube and POT.cube by Vesta and they all show normally. I do not know what happens and can you give me some tips?]]>
My charge data in FHI-aims show that in Al-doped graphene, Al has positive charge and carbons have near to zero but negative charges. In VMD, the color scale bar shows that Al has negative ESP, and C atoms have positive ESP. I have attached both figures. I think if this problem is solved, I could use the ESP figures in the paper.
Very thanks
Currently Multiwfn is mainly designed for analyzing isolated system, there is no option that can remove the upper layer. You should manually erase it using image editor.
]]>