Multiwfn

This manual is work in progress, please check regularly for updates


Multiwfn short introduction

  1. Make Multiwfn input .mwfn, .wfn, .wfx, .fch, .molden, .gms (or .cub, .grd, .pdb, .xyz, .mol - for specific purposes).

  2. 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

  3. Load enviroment:

     module use /gpfs/mariana/modules/green/chemistry/
 module load MultiWFN/3.7

  4. 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

  5. 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 green/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 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

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

In addition, the following articles should be cited depending on the analyzes performed: