The Home Page of the Molecular Workbench Software

It is simple.

If you have installed Java, clicking THIS LINK should automatically download (as small as 1.6 MB!), install, and start the Molecular Workbench software, regardless of the operating system you are using. If not, please proceed to the following instructions.

System requirements

MW runs on Windows, Mac OS X v10.4+, and Linux. The only requirement is that the Java Runtime Environment (JRE) of Java 2 Platform, Standard Edition (J2SE) v1.5 or higher version must be installed. If you are a Windows or Linux user, and have not installed the required Java software, please download or update it from java.com. The entire Java installation process is Web-based and automatic, similar to installing Macromedia Flash. Mac OS X users can update to the latest Java through the "Software Update ..." item in the menu under the Apple Logo in the screen menu bar.

If you are in a network that prevents you from installing anything (as networks in most schools do), please contact your network administrator.

Something you should know about MW:
MW is a simulation program that needs considerable horse power of your computer. It is strongly recommended that you run MW when there are no other visible programs or hidden processes (e.g. a virus scan, a backup job, and so on) running at the same time. If possible, we suggest that you also quit the currently opened programs that use a lot of computer memory. Doing so would help speed up MW and the Java Virtual Machine that supports it. You may find that MW launches slowly initially. That is because the Java Virtual Machine needs to boot before MW can run, which is a process that could take a while depending on your system. But once the Java Virtual Machine is up, MW should run faster.

MW may not run well on Windows computers older than five years, and earlier Mac OS X versions. Also, MW works the best for broadband users. If you only have dial-up access, you will probably do better if you pre-install all models and activities beforehand (use the "Option>Prefetch to Cache" menu from MW after you launch it) and choose the "Work Offline" mode from the File Menu after you have prefetched the materials you are interested in exploring.

Installation through Java Web Start

Windows

Click this link: "MW2.jnlp". After a few seconds, you should see the following window (the following images were taken from a Windows XP operating system --- the actual look will be different depending on your Windows version and settings):

When the downloading process completes, you will see the following information:

The above warning message is set to protect your computer security, NOT to push you off. It is a confirmation that the software you are downloading was sealed by us and has not been modified maliciously by someone. Please choose "Always". The message window will not pop up again next time you launch MW.

If you see a new desktop icon as follows:

MW has been installed to your system. Clicking this icon will launch MW --- you do not need the MW2.jnlp file any more.
If you do not see the desktop icon:
Right-click on this hyperlink: "MW2.jnlp", select "Save Target As..." from the popup menu, and then save the file to your desktop. Just double-click the downloaded file when you want to launch the software next time. The software has been installed onto your computer --- you do not need a browser to open it any longer.

Mac OS X (10.4 or higher)

Click this link: "MW2.jnlp". After a few seconds, you should see the following window (the following images were taken from a Mac OS X 1.4.3 operating system --- the actual look will be different depending on your OS X version):

When the downloading process completes, you will see the following information:

NOTE: This message may pop up every time you launch MW. Please click here to see how to turn it off.

Please follow these steps to continue installation:
If you see the following dialog window:

Please select "Yes". The next window you will see is:

Please select "Save". This will put MW to your desktop. You will see a desktop icon for MW:

Clicking this icon will launch MW --- you do not need the MW2.jnlp file any more. If there is an update of MW, it will download the update as well.
If nothing in the above shows up, or clicking the desktop icon does not launch MW:
Hold down the CTRL key and click on this hyperlink: "MW2.jnlp", select "Download Linked File" from the popup menu, and then save the file to your desktop. Just double-click the downloaded file when you want to launch the software next time. The software has been installed onto your computer --- you do not need a browser to open it any longer.

Installation without Java Web Start

Some of our users have reported that MW cannot be installed or launched through Java Web Start (caused by many factors, including Java bugs, their network settings, Apple updates, just to name a few). The alternative is to download the Java executable "mw.jar" to your disk and double-click on it to run MW. When you download "mw.jar", it is important that you do not rename the jar file--the file name must be exactly "mw.jar" (all lower case). If you rename the file, MW will complain about it and will not launch (this is a security measure we built into MW to protect your computer system).

Windows users

Install the latest Java software, if you have not.
Click this link to save mw.jar on your disk. Do not rename the file--the file name must be exactly "mw.jar".
Double-click once and only once on mw.jar to launch MW. On some old machines, the launching process will take a while. Please wait.
To run MW again, just double-click mw.jar. You need not repeat the first two steps when you want to run it again.
Mac OS X users

You must have OS 10.4 or higher version and Java 1.5 or higher version. If you do not have the required Java version, please update through the Software Update utility. Once you make sure that you have the required Java software, right-click or CTRL+click this link: mw.jar and save the file to your disk. Do not rename the file--the file name must be exactly "mw.jar". After downloading it, simply double-click once and only once on it to launch MW.
Linux users

You need to install the latest Java Runtime Environment first, then download the file given by the following link: mw.jar. Double-click on mw.jar to launch MW. If it does not launch, open a x-terminal, change to the directory where it is located, and type in the following command: java -jar mw.jar. If the java command is not recognized, please also include the path (e.g. /usr/local/jdk1.6/bin, if Java is installed in the /usr/local/jdk1.6 directory).

For more information about troubleshooting, please read the FAQ.

Download source code

We recommend that the Eclipse IDE be used to get the source code. You can access it through https://svn.concord.org/svn/projects/ using SVN. Once you connect to our SVN server, check out trunk/common/java/simulations/mw/. The source code can also be browsed online.

When you run it, make sure to set a system property called mw.nosecurity to be true in the launching command. Otherwise, the application will just hang. To protect your users from malicious code that could be plugged into an MW page, however, this property should not be set when you deploy your build.