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 &

3.2.3 Binary options

Available binary options can be taken from the binary help:

$ molden -h

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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