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Multiwfn
This manual is work in progress, please check regularly for updates
Multiwfn short introduction
Make Multiwfn input
.mwfn
,.wfn
,.wfx
,.fch
,.molden
,.gms
(or.cub
,.grd
,.pdb
,.xyz
,.mol
- for specific purposes).Accesse viz by remote access programs (more preferable) or by ssh protocol (less preferable):
ssh -X -Y -J UNI-ID@base.hpc.taltech.ee UNI-ID@viz
Load enviroment:
module use /gpfs/mariana/modules/green/chemistry/ module load MultiWFN/3.7
Run Multiwfn in interactive mode:
srun Multiwfn job.wfn
Multiwfn also can be run by multiwfn.slurm batch script as a non-interactive mode with pre-prepared responses:
#!/bin/bash #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --job-name=test #SBATCH --mem=2GB #SBATCH -t 1:00 #SBATCH --partition=short module load green/all module load MultiWFN/3.7 Multiwfn job.wfn << EOF > /dev/null 2 2 -4 6 0 -10 100 2 1 mol.pdb q EOF
In this case job is submitted using
sbatch
command:sbatch multiwfn.slurm
Visualize results if needed:
display job.png
or
module use /gpfs/mariana/modules/gray/spack/ module load vmd vmd job.pdb
NB! It is recommended to visualize Multiwfn results in VMD program, corresponding scripts are provided in Multiwfn examples (/gpfs/mariana/software/green/MultiWFN/Multiwfn_3.7_bin_Linux/examples/).
Multiwfn long version
Options
Multiwfn is an interactive program performing almost all of important wavefunction analyszes (showing molecular structure and orbitals, calculating real space function, topology analysis, population analysis, orbital composition analysis, bond order/strength analysis, plotting population density-of-states, plotting various kinds of spectra (including conformational weighted spectrum), quantitative analysis of molecular surface, charge decomposition analysis, basin analysis, electron excitation analyses, orbital localization analysis, visual study of weak interaction, conceptual density functional theory (CDFT) analysis, energy decomposition analysis).
For many frequently used analyszes Multiwfn has short youtube videos and “quick start” examples (/gpfs/mariana/software/green/MultiWFN/Multiwfn_3.7_bin_Linux/examples/). More information can be found in the manual.
Input
As an input Multiwfn uses output files of other quantum chemistry programs, including Gaussian, ORCA, GAMESS-US, NWChem, xtb, Turbomole. For example, .wfn
(wavefunction file), .fch
(Gaussian check file), .molden
(Molden input file), .gms
(GAMESS-US output file), .mwfn
(Multiwfn wavefunction file). Other types of files, such as such as .cub
, .grd
, .pdb
, .xyz
, .log
, .out
and .mol
files, may be used in certain cases and purposes.
Environment
On viz environment is set up by the commands:
module use /gpfs/mariana/modules/green/chemistry/
module load MultiWFN/3.7
The first time use, user has to agree to the licenses:
touch ~/.licenses/multiwfn-accepted
if this is the first user license agreement, the following commands should be given:
mkdir .licenses
touch ~/.licenses/multiwfn-accepted
NB! After agreeing to the license, user has to log out and log in again to be able run Multiwfn
.
On base environment is set up by the commands:
module load rocky8/all
module load MultiWFN/3.7
User also needs to agree with the licenses, as described above.
Running Multiwfn
NB! Since Multiwfn has a lot of functionality, we recommend that the user first study the corresponding section in the manuals (text, video) or examples (/gpfs/mariana/software/green/MultiWFN/Multiwfn_3.7_bin_Linux/examples/). This will greatly simplify the selection of answers in the interactive menu.
The best practice is to try to reproduce something from the examples folder. To do this, the corresponding files will need to be copied to the user’s derictory using the following commands:
mkdir examples
cp -r /gpfs/mariana/software/green/MultiWFN/Multiwfn_3.7_bin_Linux/examples/* examples/
NB! The user can run Multiwfn only from his own folder, not from the shared.
For visualization that does not perform additional calculations, but only reads outputs (for example spectra visualization), Multiwfn can be run in interactive mode using srun
:
srun Multiwfn job.log
or using several threads (here - 4):
srun -n 4 Multiwfn job.log
To exit interactive mode press q
key.
For jobs connected to electron density analysis especially in large systems it is recommended to run multiwfn.slurm batch script with pre-prepared responses. Below is shown slurm script for Critical Points (CPs) search using job.wfn:
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=test
#SBATCH --mem=2GB
#SBATCH -t 1:00
#SBATCH --partition=short
module load rocky8/all
module load MultiWFN/3.7
Multiwfn job.wfn << EOF > /dev/null
2
2
-4
6
0
-10
100
2
1
mol.pdb
q
EOF
Job is submitted by sbatch
command:
sbatch multiwfn.slurm
Results visualization
By default, plots made by Multiwfn will be written in the .png
format and can be visualized by command:
display job.png
Although Multiwfn has its own graphical interface, we recommend to visualize Multiwfn results in VMD (Visual Molecular Dynamics) program, corresponding scripts are provided in Multiwfn examples (/gpfs/mariana/software/green/MultiWFN/Multiwfn_3.7_bin_Linux/examples/) (with .vmd
extensions). More about visualization on viz can be found here and about VMD - here.
On base VMD environment is set up by the commands:
module load green
module load VMD
VMD is run by command vmd
:
vmd job.pdb
How to cite:
Citing the original paper of Multiwfn is mandatory - DOI: 10.1002/jcc.22885
Quantitative molecular surface analysis (main function 12) - DOI:10.1016/j.jmgm.2012.07.004
Hole-electron analysis (subfunction 1 of main function 18) - DOI:10.1016/j.carbon.2020.05.023
Electrostatic potential evaluation algorithm - DOI:10.1039/D1CP02805G
Orbital composition analysis (main function 8). - Tian Lu, Feiwu Chen, Calculation of Molecular Orbital Composition, Acta Chim. Sinica, 69, 2393-2406 (2011) (in Chinese) (http://sioc-journal.cn/Jwk_hxxb/CN/abstract/abstract340458.shtml)
Charge decomposition analysis (CDA) (main function 16) - Meng Xiao, Tian Lu, Generalized Charge Decomposition Analysis (GCDA) Method, Journal of Advances in Physical Chemistry, 4, 111-124 (2015) (in Chinese) (http://dx.doi.org/10.12677/JAPC.2015.44013)
Atomic dipole moment corrected Hirshfeld (ADCH) - DOI:10.1142/S0219633612500113
Population analysis module (main function 7) - DOI:10.3866/PKU.WHXB2012281
Laplacian bond order (LBO) - DOI: 10.1021/jp4010345
Statistical analysis of area in different ESP ranges on vdW surface - DOI:10.1007/s11224-014-0430-6
Charge-transfer spectrum - DOI:10.1016/j.carbon.2021.11.005
Electron localization function (ELF) - DOI:10.3866/PKU.WHXB20112786
Analysis of valence electron and deformation density - DOI:10.3866/PKU.WHXB201709252
Predicting binding energy of hydrogen bonds based properties of bond critical point - DOI:10.1002/jcc.26068
electron analysis based on localized molecular orbitals (e.g. subfunction 22 of main function 100) - DOI:10.1007/s00214-019-2541-z
van der Waals potential analysis (subfunction 6 of main function 20) - DOI:10.1007/s00894-020-04577-0
Interaction region indicator (IRI) (subfunction 4 of main function 20) - DOI:10.1002/cmtd.202100007
Independent gradient model based on Hirshfeld partition (IGMH) (subfunction 11 of main function 20) - DOI:10.1002/jcc.26812
ICSSZZ map (subfunction 4 in main function 200) - DOI:10.1016/j.carbon.2020.04.099
MO-PDOS map (Option -2 in main function 10) - DOI:10.1016/j.carbon.2020.05.023
Molecular polarity index (MPI) (outputted by main function 12) - DOI:10.1016/j.carbon.2020.09.048
Analysis of valence electron and deformation density - DOI:10.3866/PKU.WHXB201709252
Studying molecular planarity via MPP, SDP and coloring atoms according to ds values - DOI:10.1007/s00894-021-04884-0
Energy decomposition analysis based on force field (EDA-FF) - DOI:10.1016/j.mseb.2021.115425