JUSTUS2/Software/Molden: Difference between revisions

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{{Softwarepage|chem/molden}}

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| Links
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| [http://www.cmbi.ru.nl/molden Homepage] | [http://www.cmbi.ru.nl/molden Documentation]
| [http://www.cmbi.ru.nl/molden/ Homepage] | [http://www.cmbi.ru.nl/molden Documentation]
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| Graphical Interface
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<br>
<br>


= Versions and Availability =
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
<br>
<big>


[https://cis-hpc.uni-konstanz.de/prod.cis/ Cluster Information System CIS]

</big>
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On the command line interface of any bwHPC cluster, a list of the available versions using
'module avail chem/molden/version'.
<pre>
$ module avail chem/molden
------------------------ /opt/bwhpc/common/modulefiles -------------------------
chem/molden/5.2.1
</pre>
<br>


= Usage =
= Usage =
Once the module ''Molden'' is loaded, the binaries '''molden''' (Command-Line) and '''gmolden''' (GUI) can be directly executed:
== Loading the module ==
== Command-Line ==
You can load the default version of ''Molden'' with the command
<pre>
$ module load chem/molden
</pre>
If you wish to load a specific (older) version of ''Molden'', you can do so using e.g.
<pre>
$ module load chem/molden/5.1
</pre>
to load the version 5.1
<br>
<br>

== Software Binaries ==
=== Command-Line ===
Once the module ''Molden'' is loaded, the binaries '''molden''' and '''gmolden''' can be directly executed:
<pre>
<pre>
$ molden
$ molden
</pre>
</pre>
=== Graphical User Interface (GUI) ===
== Graphical User Interface (GUI) ==
<pre>
<pre>
$ gmolden &
$ gmolden &
</pre>
</pre>
[[File:molden_gui.jpg]]
[[File:molden_gui.jpg]]

==== Binary options ====
Available binary options can be taken from the binary help:
<pre>
$ 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
</pre>
or from the [http://www.cmbi.ru.nl/molden/command.html website].
<br>
<br>

= 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'.
<pre>
$ 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
$
</pre>
<br>

= Examples =
To visualize the cartesian coordinates of one molecule stored in the file ''molecule.xyz'' without automatic conversion to Z-matrix, execute:
<pre>
$ molden -a molecule.xyz
</pre>
<br>

= Version-Specific Information =
For specific information about a special version , see the information available via the module system with the command
<pre>
$ module help chem/molden/version
</pre>
<br>

----
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]

Latest revision as of 10:00, 23 April 2024

The main documentation is available via module help chem/molden on the cluster. Most software modules for applications provide working example batch scripts.


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

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.


Usage

Once the module Molden is loaded, the binaries molden (Command-Line) and gmolden (GUI) can be directly executed:

Command-Line

$ molden

Graphical User Interface (GUI)

$ gmolden &

Molden gui.jpg

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