vmd_script

These VMD 1.9.3 scripts are used to draw beautiful graphs on wavefunction analysis. Scripts are used to process the output of multiwfn and ORCA. Most of multiwfn scripts were modified from Sobereva (http://sobereva.com/multiwfn/), and the original scripts were available from the installation package of Multiwfn.

Basic Configuration

1. Copy these .vmd files to installation directory of VMD 1.9.3.
2. Add following commands to vmd.rc.

   source showcub.vmd
   source showapt.vmd
   source showpole.vmd
   source showvib.vmd
   source showorb.vmd
   source showfod.vmd
   source showaim.vmd
   source showbas.vmd
   source showesp.vmd
   source showalie.vmd
   source showhirsh.vmd
   source showrdg.vmd
   source showigm.vmd
   source showanci.vmd
   

Basic Usage

1. Generate required cub/pdb/pqr/xyz/txt files by Multiwfn/ORCA.
2. Move those cub/pdb/pqr/xyz/txt files to the installation directory of VMD 1.9.3.
3. Open a new VMD window.
4. Input required command in VMD Command-Line Window.

Function	Command	Required Files
View cub file	cub xxx	xxx.cub
View atom properties	apt xxx	xxx.pqr
View atom dipole	dip xxx	xxx.xyz, multiple.txt, atom_moment.txt
View atom quadrupole	quadp xxx	xxx.xyz, multiple.txt, atom_moment.txt
View vibration modes	vib xxx n	xxx.xyz, xxx.out
View orbitals	orb	orbital.cub
view FOD plot	fod xxx	xxx.eldens.cube
View ESP surface	esp	mapfunc.cub, surf.cub, surfanalysis.pdb
View ESP surface	esppt	mol.pdb, vtx.pdb, surfanalysis.pdb
View vdWP surface	vdwp	vdW.cub
View ALIE surface	alie	mapfunc.cub, surf.cub, surfanalysis.pdb
View LEA surface	lea	mapfunc.cub, surf.cub, surfanalysis.pdb
View Hirshfeld surface	hirshd	mapfunc.cub, surf.cub, surfanalysis.pdb
View Hirshfeld surface	hirshr	mapfunc.cub, surf.cub, surfanalysis.pdb
View Becke surface	becked	mapfunc.cub, surf.cub, surfanalysis.pdb
View Becke surface	becker	mapfunc.cub, surf.cub, surfanalysis.pdb
View Basins	basin	mol.pdb, attractors.pqr
AIM topology analysis	aim	mol.pdb, CPs.pdb, paths.pdb
RDG analysis	rdg	func1.cub, func2.cub
IRI analysis	iri	func1.cub, func2.cub
DORI analysis	dori	func1.cub, func2.cub
IGM analysis	igminter	sl2r.cub, dg_inter.cub
IGM analysis	igmintra	sl2r.cub, dg_intra.cub
aRDG analysis	ardg	avgsl2r.cub, avgRDG.cub
aRDG analysis	ardgtfi	thermflu.cub, dg_intra.cub
aIGM analysis	aigm	avgsl2r.cub, avgdg_inter.cub
aIGM analysis	aigmtfi	thermflu.cub, avgdg_inter.cub

Useful Tips

• Use the command helpp to get commands available in the current script.
• In some scripts, the display styles (colors, materials), isosurface values, lower and upper limits of color scale can be changed via commands, using helpp for more information.
• In some scripts, the labels can be added via commands like labcp all and removed via command labcp no. Some useful information such as critical point indexes, atoms properties, ESP extrema, ALIE extrema, LEA extrema, Hirshfeld surface extrema, Becke surface extrema are given in the labels.
• In script apt xxx, cubes can be added via commands like cubadd cubname and removed via command cubdel. Files request: cubname.cub
• In script apt xxx, orbitals can be added via commands like orbadd 1 3 and removed via command orbdel. Files request: orb000001.cub, orb000002.cub, orb000003.cub
• In script aim and basin, basins can be added via commands like basinadd 1 3 and removed via command basindel. Files request: basin0001.cub, basin0002.cub, basin0003.cub
• In script rdg, iri, dori, igminter, and igmintra, critical points and topology paths can be added via commands aimadd. Files request: CPs.pdb, paths.pdb