Difference between revisions of "JUSTUS2/Software/Molden"
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| − | = Versions and Availability = |
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| − | A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the |
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| − | <br> |
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| − | <big> |
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| − | [https://cis-hpc.uni-konstanz.de/prod.cis/ Cluster Information System CIS] |
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| − | |||
| − | </big> |
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| − | {{#widget:Iframe |
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| − | |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/molden |
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| − | |width=99% |
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| − | |height=150 |
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| − | |border=0 |
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| − | }} |
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| − | On the command line interface of any bwHPC cluster, a list of the available versions using |
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| − | 'module avail chem/molden/version'. |
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| − | <pre> |
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| − | $ module avail chem/molden |
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| − | ------------------------ /opt/bwhpc/common/modulefiles ------------------------- |
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| − | chem/molden/5.2.1 |
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| − | </pre> |
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| − | <br> |
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= Usage = |
= Usage = |
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| + | Once the module ''Molden'' is loaded, the binaries '''molden''' (Command-Line) and '''gmolden''' (GUI) can be directly executed: |
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| − | == Loading the module == |
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| + | == Command-Line == |
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| − | You can load the default version of ''Molden'' with the command |
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| − | <pre> |
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| − | $ module load chem/molden |
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| − | </pre> |
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| − | If you wish to load a specific (older) version of ''Molden'', you can do so using e.g. |
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| − | <pre> |
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| − | $ module load chem/molden/5.1 |
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| − | </pre> |
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| − | to load the version 5.1 |
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| − | <br> |
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| − | <br> |
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| − | |||
| − | == Software Binaries == |
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| − | === Command-Line === |
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| − | Once the module ''Molden'' is loaded, the binaries '''molden''' and '''gmolden''' can be directly executed: |
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<pre> |
<pre> |
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$ molden |
$ molden |
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</pre> |
</pre> |
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| − | + | == Graphical User Interface (GUI) == |
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<pre> |
<pre> |
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$ gmolden & |
$ gmolden & |
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[[File:molden_gui.jpg]] |
[[File:molden_gui.jpg]] |
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| − | ==== Binary options ==== |
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| − | Available binary options can be taken from the binary help: |
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| − | <pre> |
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| − | $ molden -h |
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| − | -a no automatic cartesian -> zmat conversion |
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| − | -b use orbitals of first point on opt. runs |
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| − | -c 0.5 change depth of shading, range [0.0-1.0] |
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| − | -e DMAREL INPUT: Use est set of parameters |
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| − | -f PDB: build connectivity from cartesian coordinates |
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| − | -g PDB: always calculate Helix/Sheet information |
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| − | -geom XXXxYYY-xxx-yyy |
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| − | XXX and YYY are the size of the window |
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| − | xxx and yyy are the position of the window |
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| − | -h print commandline flags |
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| − | -hoff switch of hydrogen bonds |
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| − | -hdmin x mininum hydrogen bond distance (Ang) |
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| − | -hdmax x maximum hydrogen bond distance (Ang) |
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| − | -hamin x mininum hydrogen bond angle (Degrees) |
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| − | -hamax x maximum hydrogen bond angle (Degrees) |
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| − | -i opt fdat files: |
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| − | opt=1 standardise H-C, H-N |
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| − | opt=2 1 + standardise phenyl rings |
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| − | -j num maximum number of gifs to write |
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| − | -k num select color of labels (0-15) |
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| − | (gmolden only). |
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| − | -l dont display molden logo |
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| − | -n dont add hydrogens to PDB file |
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| − | -m turn off the beep sounds |
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| − | -o fname plotfilename (default=plot) |
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| − | -p 2.0 change perspective value (def: 13.0) |
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| − | -r fname read file with per line; |
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| − | atom color(1-15) VandeWaalsRadius, (- = skip) |
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| − | background color(1-15) |
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| − | palette red #CF54FD ... (14 colors) |
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| − | -s 4.0 scale amplitude of normal vibrations |
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| − | -t read ascii MOPAC93 Chem3D style |
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| − | -u With GAMESS-US optimisation output, molden |
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| − | generates a z-matrix, (def: read from output) |
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| − | -v print verbose information |
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| − | -w opt write all points of a movie to a file: |
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| − | opt specifies format; xyz(=1) zmat(=2,mopac) |
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| − | VRML2.0(=3) |
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| − | -x file read in file with spherical atomic densities |
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| − | -y 1.0 threshold for printing displacement vectors |
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| − | of normal modes to postscript file |
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| − | -z create high quality opengl coils |
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| − | -A Keep order of atoms when creating a Z-matrix |
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| − | -C Color postscript (default=mono, except PDB) |
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| − | -D opt DMA mode: |
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| − | 0 = atomic sites only (default) |
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| − | 1 = atomic+halfway-bond sites |
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| − | 2 = no shift of overlap dens. of conn. atoms |
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| − | -E DMAREL input: use coordinates from multipoles |
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| − | -F gmolden: Use all opengl code, (line drawing) |
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| − | -G 0.6 Grid width colour coded ESP potential map |
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| − | -H GAMESS-US: do normal modes when HSSEND=.TRUE. |
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| − | -I dont use shaders, if available |
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| − | -J opt Choose format of screen shot: |
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| − | 1 = GIF (default) |
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| − | 2 = RGB |
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| − | 3 = BMP |
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| − | -L display both neg. and pos. contour in space |
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| − | plot of the laplacian |
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| − | -1 use only the lower half of the cubic grid |
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| − | used for the space type plot |
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| − | -2 use only the upper half of the cubic grid |
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| − | used for the space type plot |
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| − | -M MonoChrome postscript |
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| − | -N Check for mpi, to run ambfor/ambmd |
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| − | in parallel |
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| − | -O switch off multiple structures handling |
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| − | -P PDB: treat all input files as PDB files |
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| − | -Q support for older StarNet xwin32 (ver. 6) |
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| − | -R npts adjust the gridsize in points |
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| − | -S start with shade off |
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| − | -T treat all input files as TINKER xyz files |
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| − | -U do not use opengl shaders |
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| − | -X use with XMOL cartesian format input |
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| − | -V fname VRML density filename |
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| − | -W Write VRML2.0 instead of VRML1.0 |
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| − | -Z Map the Z-matrix file mapfile onto crystal |
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| − | mapfile contains Z-matrix followed by keyword |
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| − | MAP and per line an integer that maps a |
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| − | Z-matrix line onto a cartesian line |
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| − | -= Use gamess-us dialect of gaussian zmat writing |
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| − | </pre> |
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| − | or from the [http://www.cmbi.ru.nl/molden/command.html website]. |
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| − | <br> |
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| − | <br> |
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| − | = Molden-Specific Environments = |
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| − | To see a list of all Molden environments set by the 'module load chem/molden/version'-command, |
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| − | use 'env | grep MOLDEN' |
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| − | Or try the command 'module show 'chem/molden/version'. |
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| − | <pre> |
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| − | $ module load chem/molden |
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| − | $ env | grep MOLDEN |
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| − | MOLDEN_VERSION=5.2.1 |
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| − | MOLDEN_AMB_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin/ambfor |
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| − | MOLDEN_BIN_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin |
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| − | MOLDEN_UTL_DIR=/opt/bwhpc/common/chem/molden/5.2.1/utils |
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| − | MOLDEN_SRF_DIR=/opt/bwhpc/common/chem/molden/5.2.1/bin/surf |
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| − | $ |
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| − | </pre> |
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| − | <br> |
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| − | |||
| − | = Examples = |
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| − | To visualize the cartesian coordinates of one molecule stored in the file ''molecule.xyz'' without automatic conversion to Z-matrix, execute: |
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| − | <pre> |
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| − | $ molden -a molecule.xyz |
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| − | </pre> |
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| − | <br> |
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| − | |||
| − | = Version-Specific Information = |
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| − | For specific information about a special version , see the information available via the module system with the command |
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| − | <pre> |
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| − | $ module help chem/molden/version |
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| − | </pre> |
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| − | <br> |
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---- |
---- |
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Revision as of 10:31, 16 December 2021
| 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 Usage
Once the module Molden is loaded, the binaries molden (Command-Line) and gmolden (GUI) can be directly executed:
2.1 Command-Line
$ molden
2.2 Graphical User Interface (GUI)
$ gmolden &
