JUSTUS2/Software/Molden

Description	Content
module load	chem/molden
Availability	bwUniCluster | BwForCluster_Chemistry
License	Free. See: Copyright CMBI
Citing	Molden-Reference
Links	Homepage | Documentation
Graphical Interface	Yes

1 Description

Molden is a software package for displaying molecular coordinates, molecular orbitals, electron densities from various quantum chemical software packages and supports contour and 3-D grid plots. Moreover, Molden supports many output formats including postscript, povray, OpenGL and hpgl.

2 Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS

{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/molden |width=99% |height=200 |border=1 }}

Open the above links by using the right mouse button and select "open in a new window" or "open in a new tab".

On the command line interface of any bwHPC cluster, a list of the available versions using 'module avail chem/molden/version'.

$ module avail chem/molden
------------------------ /opt/bwhpc/common/modulefiles -------------------------
chem/molden/5.2.1

3 Usage

3.1 Loading the module

You can load the default version of Molden with the command

$ module load chem/molden

If you wish to load a specific (older) version of Molden, you can do so using e.g.

$ module load chem/molden/5.1

to load the version 5.1

3.2 Software Binaries

3.2.1 Command-Line

Once the module Molden is loaded, the binaries molden and gmolden can be directly executed:

$ molden

3.2.2 Graphical User Interface (GUI)

$ gmolden &

3.2.2.1 Binary options

Available binary options can be taken from the binary help:

$ molden -h
 -a        no automatic cartesian -> zmat conversion
 -b        use orbitals of first point on opt. runs
 -c 0.5    change depth of shading, range [0.0-1.0]
 -e        DMAREL INPUT: Use est set of parameters
 -f        PDB: build connectivity from cartesian coordinates
 -g        PDB: always calculate Helix/Sheet information
 -geom XXXxYYY-xxx-yyy
           XXX and YYY are the size of the window
           xxx and yyy are the position of the window
 -h        print commandline flags
 -hoff     switch of hydrogen bonds
 -hdmin x  mininum hydrogen bond distance (Ang)
 -hdmax x  maximum hydrogen bond distance (Ang)
 -hamin x  mininum hydrogen bond angle (Degrees)
 -hamax x  maximum hydrogen bond angle (Degrees)
 -i opt    fdat files: 
           opt=1 standardise H-C, H-N
           opt=2 1 + standardise phenyl rings
 -j num    maximum number of gifs to write
 -k num    select color of labels (0-15)
           (gmolden only).
 -l        dont display molden logo
 -n        dont add hydrogens to PDB file
 -m        turn off the beep sounds
 -o fname  plotfilename (default=plot)
 -p 2.0    change perspective value (def: 13.0)
 -r fname  read file with per line; 
           atom color(1-15) VandeWaalsRadius, (- = skip)
           background color(1-15)
           palette red #CF54FD ...   (14 colors)
 -s 4.0    scale amplitude of normal vibrations
 -t        read ascii MOPAC93 Chem3D style
 -u        With GAMESS-US optimisation output, molden
           generates a z-matrix, (def: read from output)
 -v        print verbose information
 -w opt    write all points of a movie to a file:
           opt specifies format; xyz(=1) zmat(=2,mopac)
           VRML2.0(=3)
 -x file   read in file with spherical atomic densities
 -y 1.0    threshold for printing displacement vectors
           of normal modes to postscript file
 -z        create high quality opengl coils
 -A        Keep order of atoms when creating a Z-matrix
 -C        Color postscript (default=mono, except PDB)
 -D opt    DMA mode:
           0 = atomic sites only (default)
           1 = atomic+halfway-bond sites
           2 = no shift of overlap dens. of conn. atoms
 -E        DMAREL input: use coordinates from multipoles
 -F        gmolden: Use all opengl code, (line drawing)
 -G 0.6    Grid width colour coded ESP potential map
 -H        GAMESS-US: do normal modes when HSSEND=.TRUE.
 -I        dont use shaders, if available
 -J opt    Choose format of screen shot:
           1 = GIF (default)
           2 = RGB
           3 = BMP
 -L        display both neg. and pos. contour in space
           plot of the laplacian
 -1        use only the lower half of the cubic grid
           used for the space type plot
 -2        use only the upper half of the cubic grid
           used for the space type plot
 -M        MonoChrome postscript
 -N        Check for mpi, to run ambfor/ambmd 
           in parallel 
 -O        switch off multiple structures handling
 -P        PDB: treat all input files as PDB files
 -Q        support for older StarNet xwin32 (ver. 6)
 -R npts   adjust the gridsize in points
 -S        start with shade off
 -T        treat all input files as TINKER xyz files
 -U        do not use opengl shaders
 -X        use with XMOL cartesian format input
 -V fname  VRML density filename
 -W        Write VRML2.0 instead of VRML1.0
 -Z        Map the Z-matrix file mapfile onto crystal
           mapfile contains Z-matrix followed by keyword
           MAP and per line an integer that maps a
           Z-matrix line onto a cartesian line
 -=        Use gamess-us dialect of gaussian zmat writing

or from the website.

4 Molden-Specific Environments

To see a list of all Molden environments set by the 'module load chem/molden/version'-command, use 'env | grep MOLDEN' Or try the command 'module show 'chem/molden/version'.

$ module load chem/molden
$ env | grep MOLDEN
MOLDEN_VERSION=5.2.1
MOLDEN_AMB_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin/ambfor
MOLDEN_BIN_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin
MOLDEN_UTL_DIR=/opt/bwhpc/common/chem/molden/5.2.1/utils
MOLDEN_SRF_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin/surf
$ 

5 Examples

To visualize the cartesian coordinates of one molecule stored in the file molecule.xyz without automatic conversion to Z-matrix, execute:

$ molden -a molecule.xyz

6 Version-Specific Information

For specific information about a special version , see the information available via the module system with the command

$ module help chem/molden/version

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