Difference between revisions of "JUSTUS2/Software/Molden"
m (→Graphical User Interface (GUI)) |
m (→Binary options) |
||
Line 82: | Line 82: | ||
<pre> |
<pre> |
||
$ molden -h |
$ 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> |
</pre> |
||
or from the [http://www.cmbi.ru.nl/molden/command.html website]. |
or from the [http://www.cmbi.ru.nl/molden/command.html website]. |
Revision as of 18:29, 30 November 2015
Description | Content |
---|---|
module load | chem/molden |
Availability | bwUniCluster | BwForCluster_Chemistry |
License | Free. See: Copyright CMBI |
Citing | Molden-Reference |
Links | Homepage | Documentation |
Graphical Interface | Yes |
Contents
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 $ -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