Java simulations are no longer supported

Legacy Java

For users who cannot run the web simulations, we are providing legacy access the Java-based version of these simulations.

Note that this is provided purely for archival purposes and will not be actively supported. We will also include legacy support materials to troubleshoot common problems that were documented during active use of the Java simulations.

Using the Legacy Java Files

You can put the ConnectedChemistry.jar file anywhere on your hard drive, whether on your desktop, an apps folder, or another directory. However, if you’re having trouble, put this file alone in a folder by itself, so other, older files don’t interfere.

If you attempt to launch the ConnectedChemistry.jar file directly from a CD, the Simulation will not work.

The ConnChem Simulations actually require two files to run:

  • ConnectedChemistry.jar
  • chemdb

If you don’t have the second file, don’t panic: when you run the “ConnectedChemistry.jar” file, it will create the “chemdb” file in the same folder for you. In fact, it’s best if the “ConnectedChemistry.jar” file is alone in whatever folder you put it in. This will prevent you from using an old, obsolete database from an earlier release.

I fact, when you download the software, it’s best if you delete any files named chemdb you can find. Don’t worry… the system will make a new one when it needs to. This doesn’t mean you have to delete chemdb each time you run the file, but with a new version it’s best to start from scratch.

Do not rename any files. Sometimes if you are downloading ConnectedChemistry.jar to a crowded downloads folder, there may already be an older file with the same name, in which case your system will rename ConnectedChemistry.jar to something else, like “ConnectedChemistry-1.jar“. This won’t work. Rename the file to “ConnectedChemistry.jar” and follow the instructions below.

To run the software, follow these steps exactly

  1. create a new folder on your desktop, named whatever you like (ConnChem is a good choice)
  2. drag the file ConnectedChemistry.jar into your new folder. It should now be alone in this folder.
  3. double-click on the ConnectedChemistry.jar file in your new folder. This should automatically create the database “chemdb” in the same folder, and the software will run.

Recommended specifications

Java 6 Runtime Environment

      Windows           macOS

Troubleshooting

What should I do if my simulation window is flashing?

This could be caused by the simulation competing for system resources. Try shutting down any running background applications and relaunch the simulation file.

What if I don't see any molecules in my simulation?

This may be caused by having an outdated or corrupted database file. Locate the existing copy of chemdb, delete it, and relaunch ConnectedChemistry.jar.

This may also be the result of having multiple copies of simulation downloaded. Be sure that the simulation file is named ConnectedChemistry.jar, and not some variant like ConnectedChemistry-1.jar or ConnectedChemistry (1).jar. Renaming the simulation file to ConnectedChemistry.jar may fix this problem.

If you still can't run the software, you may have to contact your system administrator

Make sure you have the legacy Java 6 JRE (Java Runtime Environment) installed: https://www.oracle.com/java/technologies/javase-java-archive-javase6-downloads.html

On Windows, Make sure .jar files are registered as Java executables (not as archives). If installing the legacy runtime does not fix your issue, your system administrator may also try these steps:

  1. Open the Windows Explorer, from the Tools select ‘Folder Options…’
  2. Click the File Types tab, scroll down and select JAR File type.
  3. Press the Advanced button.
  4. In the Edit File Type dialog box, select open in Actions box and click Edit…
  5. Press the Browse button and navigate to the location the Java interpreter javaw.exe.
  6. In the Application used to perform action field, needs to display something similar to
    C:\Program Files\Java\j2re1.4.2_04\bin\javaw.exe” -jar “%1” %
    (Note: the part starting with ‘javaw’ must be exactly like that; the other part of the path name can vary depending on which version of Java you’re using) then press the OK buttons until all the dialogs are closed.

Alternatively, this may work instead (on Windows). This doesn’t seem to be an issue with Macintosh computers.