JUSTUS2/Software/Molden: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
K Siegmund (talk | contribs) No edit summary |
||
(7 intermediate revisions by 2 users not shown) | |||
Line 1: | Line 1: | ||
{{Softwarepage|chem/molden}} |
|||
{| width=600px class="wikitable" |
{| width=600px class="wikitable" |
||
|- |
|- |
||
Line 5: | Line 7: | ||
| module load |
| module load |
||
| chem/molden |
| chem/molden |
||
|- |
|||
| Availability |
|||
| [[bwUniCluster]] | [[BwForCluster_Chemistry]] |
|||
|- |
|- |
||
| License |
| License |
||
Line 26: | Line 25: | ||
<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> |
|||
{{#widget:Iframe |
|||
|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/molden |
|||
|width=99% |
|||
|height=150 |
|||
|border=0 |
|||
}} |
|||
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) == |
|||
<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 |
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 &