Difference between revisions of "Molden"

Latest revision as of 21:47, 20 February 2017

Description

From Molden Documentation: Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac

Version

4.9

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

Molden requires the following module file to run:

apps/molden/4.9

See Modules for more information.

Running Molden on CIRCE/SC

The Molden user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Starting the Application

Establishing a GUI connection to CIRCE/SC

To use Molden, you will need to connect to CIRCE/SC with GUI redirection, either using:

CIRCE/SC Desktop Environment
SSH with X11 redirection
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
  - ```
  [user@localhost ~]$ ssh -X circe.rc.usf.edu
```
  or
- ```
[user@localhost ~]$ ssh -X sc.rc.usf.edu
```

Once connected to CIRCE/SC, you can open Molden using the steps below:

[user@login0 ~]$ module add apps/molden/4.9
[user@login0 ~]$ gmolden

Documentation

Home Page, User Guides, and Manuals

Molden Home Page
- http://www.cmbi.ru.nl/molden/

Reporting Bugs

Report bugs with Molden to the IT Help Desk: rc-help@usf.edu

@@ Line 1: / Line 1: @@
 == Description ==
-''From Molden Documentation:'' Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac
+''From Molden Documentation:'' '''Molden''' is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac
-== Version ==
+{{AppStandardHeader|4.9|molden}}
-*4.9
-== Authorized Users ==
+{{AppRunningOnAll}}
-*<code>CIRCE</code> account holders
-== Platform ==
-*<code>CIRCE</code> cluster
-== Running Molden on CIRCE ==
-=== [[Modules]] ===
-Molden requires the following module file to run:
-*<code>apps/molden/4.9</code><br />See [[Modules]] for more information.
 === Starting the Application ===
-Molden is quite easy to execute on CIRCE:
+{{X11Connection}}
-Before you login to <code>CIRCE</code>, you need to make sure you have X11 Forwarding enabled. If you’re logging in from a UNIX/Linux system, you will need to do the following:
+Once connected to CIRCE/SC, you can open {{PAGENAME}} using the steps below:
-<pre style="white-space:pre-wrap; width:35%; border:1px solid lightgrey; background:#000000; color:white;">
+<pre style="white-space:pre-wrap; width:40%; border:1px solid lightgrey; background:#000000; color:white;">[user@login0 ~]$ module add apps/molden/4.9
-ssh -Y user@circe.rc.usf.edu</pre>
+[user@login0 ~]$ gmolden</pre>
-Simply type <code> gmolden </code> at the command prompt AFTER loading the proper module (see above) in your terminal window. If you have properly configured an X11 session, you should see the full GMolden interface.
-For Windows, Mac, and Linux users, GMolden can also be launched through the CIRCE Desktop Environment using a terminal. For more information about the CIRCE Desktop Environment, please see our [[CIRCE Desktop|CIRCE Desktop Environment]] documentation.
+{{Documentation}}
+*Molden Home Page
+**http://www.cmbi.ru.nl/molden/
 {{ReportingBugs}}