MW runs on Windows, Mac OS X and Linux, provided that a Java Runtime Environment (JRE) 1.5 or newer versions is installed. If you are using Windows and are not sure about this, go to java.com and the Web site will automatically install the latest Java software, just like you install a Flash player to a browser. If you are a Mac OS X user, please run the "Software Update" wizard under the Apple Menu.
MW and the Java Virtual Machine that supports it need considerable computing horse power to run. You may not enjoy running it on machines older than 5 years (e.g. Windows 98).
It is likely that the cached MW application files somehow got corrupted on your disk. Try removing the files and starting again. There are two types of files that may need to be removed:
Open MW and select "Help > Uninstall Molecular Workbench via Java Cache Viewer". You will see the Java Cache Viewer dialog. Select "Molecular Workbench" and hit the removal button.
There are four reasons why the Quicktime plugin may give an error (Note: #1 and #2 below only apply to the Windows operating system):
No. You need to be able to install it to the computer. Contact your system administrator if you cannot install software (computer labs in most schools typically do not allow an average user to install ANYTHING to the machines).
More information about why MW is not an applet (if you ever care): MW is a standalone application aiming to become a Word-like program for creating simulations and simulation-based educational materials. A browser environment is too restricted to support typical authoring. People often needs to know some Javascript in order to do browser-based authoring, since Javascript is often needed to configure applets. On the other hand, a browser environment is good to deliver content. So we decided to take advantages from both browser and word processor. As a result, MW becomes a hybrid of a special browser and a Word-like authoring system.
The content in the concord.org domain is licensed under a Creative Commons Attribution-NonCommercial 3.0 License. You are free to copy, distribute, display, and perform the work to make derivative works Under the following conditions: (1) Attribution. You must attribute the materials developed by Concord Consortium in the manner specified by the author or licensor. (2) Noncommercial. You may not use this work for commercial purposes without a permission from the Concord Consortium. This license, however, does not apply to any materials you create on your own using the Molecular Workbench's modeling and authoring system, provided that they are not just copied vertabim et literatim or derived from existing materials of other authors who reserve their rights.
Many schools do not have unlimited Internet bandwidth for each student. Therefore you may want to consider downloading MW and its accompanying materials, and using them locally.
Please follow the steps below to download a self-contained version of MW materials:
Note that all the materials you download as described above cannot automatically update themselves. If you need to update them in the future, just remove the old "cd" (or whatever you have renamed it to) folder, revisit this page and redo the above steps.
With this special offline version of MW, you will not be able to access the latest simulations and activities. Nor can you collect student data. This should be used as the last resort when you encounter unsolvable problems in your school's network (firewall issues, bandwidth limitation, etc.).
If you link to a MW page directly, it will be opened using a web browser, which displays it as a page that is unreadable to most people (known as XML). To get MW to open the page, you need to do some extra work, as described in the following.
First, navigate to the page with MW. Select "Create a Launching URL in System Clipboard" under the
File Menu of MW. A URL link will be created in the System Clipboard, which can be pasted into
your web page as the href attribute of the link. Once the link is clicked, MW will
be called to open the corresponding MW page.
The above instruction applies to MW Version 2.0. If you are working with Version 1.3, you have to create a JNLP launching file and also upload the file to your web folder, together with the HTML page that references it.
Right-click (Windows/Linux) or CTRL-click this link, and then select the corresponding item from the pop-up menu to save the file to the folder where your PowerPoint or Word file is located. You perhaps also want to rename the file (if you rename the file, note that the file name needs to have .jnlp extension). After that, open the file using a text editor (such as Notepad on Windows), and scroll to the end of the file. You should see the following three lines:
<application-desc main-class="org.concord.modeler.ModelerLauncher">
<argument>remote</argument>
</application-desc>
Now, insert a line below <argument>remote</argument>, in which you must place the URL or file location of the MW page within a pair of <argument> tags:
<application-desc main-class="org.concord.modeler.ModelerLauncher">
<argument>remote</argument>
<argument>PUT URL OR FILE LOCATION HERE</argument>
</application-desc>
After saving the file, you can add link it in your PowerPoint or Word file. When the link is clicked, the MW page that you specify in the JNLP file will be opened.
Select the "Reset Desktop Launcher" item from the Help Menu, or go to the MW web page to click the "Launch MW V2.0" Button, or simply click this link to correct the problem now.
Most molecular visualization tools display molecular structures without letting users change them. MW is designed with the goal of not only visualizing structures, but also constructing structures (existing or non-existing) and simulating the physical and chemical processes they will undergo. In a typical visualization, students have to infer what is going on between static frames of structures. Whereas in MW, phenomena just emerge from dynamical simulations, and thus the gap can be filled (we hope).
On the one hand, Jmol is used in MW to render 3D view and display molecules. On the other hand, MW can be used by Jmol users to rapidly create molecules and structures, and run molecular dynamics simulation and/or energy minimization to make sense of the created structures. The molecular structures you have created and simulated can be exported in the XYZ format, which can be displayed by the Jmol applet without having to use MW. Therefore, MW can be used as a companion tool with Jmol ------ to create structures that do not yet exist (such as hypothetical nanomachines). See this page for an example.
We agree that atoms are not spherical. More than ten years ago, IBM had manipulated atoms and shown nice STM images, which reveals that the atomic world is by no mean composed of ball-like hard spheres. However, many chemistry educators have long used static ball-and-stick models, physical or computer, to teach chemistry. Those models traditionally use color balls to represent atoms. In our study, we also suspect that non-science majors who have learned through those models could have a chance to walk away with the misconception that atoms resemble balls and have colors, if the issue you raised here is not properly addressed.
Now that we know that atoms are not spheres, what is the value of a ball representation of atoms? From a pragmatic point of view, an atom can be represented by a dot, which is approximately at the location of the nucleus. This dot carries most of the mass that belongs to the atom, and therefore can be used to locate it. Now, can we say that if we have the information about all these dots of a molecule, its structure (and therefore its functions) can be determined? We know this is a very complicated question to research. But so far, it looks like that we are pretty sure that this is a good approximation. In other words, the ball-and-stick model, which can be regarded just as an overlay of balls on top of the dots and sticks connecting them, conveys the idea of chemical bonding and molecular structure, without having to overwhelm younger students with the complicated pictures of atomic and molecular orbitals that they are probably not ready to grasp.
A structural model of atoms and molecules is not the end of the story in scientific research. We want to learn how molecules behave and function. What we define as a phenomenon at the molecular level is in fact a process of atoms moving and exchanging bonding partners. Hence, the information about how atoms change with respect to time would be critical to understand how stuff works at molecular level. This is where molecular dynamics comes into play --- to simulate the time evolution of molecules under interactions.
The most advanced computational physics method for simulating dynamical processes of molecules is the Car-Parrinello method (or the many other quantum molecular dynamics methods it has inspired), which is based on solving the coupled Schrödinger/Newton equations for the electron-nucleus system. See Wikipedia for more information.
Quantum molecular dynamics is very computationally intensive and it seems to be out of the question to do on widely available computers. In the old days when Cray machines dominated at high-performance computing, however, researchers used classical molecular dynamics to simulate atoms and molecules, and the methods are still used today to simulate engineering problems.
Classical molecular dynamics is what we use in Molecular Workbench, as it is much cheaper to do computationally.
In classical molecular dynamics, atoms are simplified as point masses and the interatomic interactions are simplified using some mathematical functions, which simulate the effect of the interactions to a qualitative accuracy. These simplifications strip off the basic complexity of individual atoms as quantum entities. But under the conditions that we care about the collective behaviors of many atoms, it is an acceptable simplification. Indeed, for many nano-scale phenomena we are interested in physics, chemistry and biology, a coarse-grained atomic model serves decently. To give you a quick idea, gas laws can be nicely demonstrated by this grade of models without having to worry about if we have missed the accuracy of atomic orbitals.
The problems that follow as we try to make science comprehensible at different levels are quite general and subtle. It is probably hard for students to understand what a coarse-grained approach is and the necessities of using it in presenting knowledge. It turns out that such an approach is very important in the history of science. One day man will know that the current atomic theory is wrong at the atomic scale down, perhaps well below the level of the quark, as the string theory has been suggesting.
But this doesn't mean the atomic theory is wrong at the level where it is properly put, just as quantum mechanics doesn't overthrow classical mechanics at the level where the driving forces resulting from the motion of electrons can be approximated by empirical forces, such as the van der Waals forces at nano-scale and friction forces at micron-scale. And being empirical is perhaps not a scientific guilt. The fact that we may not even know exactly what cause Coulomb interactions between charges today does not mean that Coulomb's Law is false.
The MW software you have downloaded is the software that displays and runs models and simulations. It doesn't contain any model and simulation in the downloaded file. Materials are provided to you separately through the Internet. To access them, MW must be allowed to connect to the Internet.
Schools have various proxy servers that may cause connection issues. In theory, Java will pick up whatever proxy settings you have used for the browser and pass them to MW. In practice, however, this is not often the case. If MW reports an error that it is unable to connect to the server, it is most likely that it needs appropriate proxy settings. A simple test would be to click the link of the internal home page of MW: http://mw2.concord.org/public/index.cml. If this link opens an XML file in your browser, then your browser has been set up correctly with the proxy server. Copy the URL to MW's address field and hit ENTER. If MW reports an error, then MW hasn't been set up with the proxy server.
There are two ways of setting up MW with a proxy server. The first is to open the Preferences Dialog of MW, select the "Connection" tab and fill in the proxy information in the dialog window. This requires that each user must do this for his/her software. An alternative is to create a batch file that contains the following line of command:
java -Dhttp.proxyHost=XXX -Dhttp.proxyPort=XXX -DproxySet=true -jar mw.jar
Note that you must fill in the name of your proxy server (e.g. proxy.someone.com) and the port number in the places marked by XXX. Also note that you must download mw.jar, and the batch file must be stored in the same directory with mw.jar. If the batch file and mw.jar are placed in a network drive that every student can access, then they can just click the batch file to launch MW without having to set up the proxy information individually.
When you are using a wireless network, the chance your computer gets disconnected temporarily from the Internet is very high, especially in the case that the network is shared by many users. The software does not currently deal with this kind of connection problem well enough. The workaround of this is that you can prefetch everything you need (using "Option > Prefetch to Cache") and set the software to run in the offline mode (selecting "File > Work Offline"). Under this mode, the software will not request internet connection.
If you need to submit a report or model, however, you will still need a good network connection. The above workaround does not solve the problem in those cases.
The graphics support of the Java environment slows down significantly when a notebook computer of certain type runs on battery (possibly because when the power is unplugged, the graphics acceleration card is somehow also turned off for Java). Sometimes, even disabling the battery-saving mode does not help to reconnect Java with the graphics acceleration card. Currently, plugging in power is the only solution we can recommend. This happens only on some Windows XP machines. Mac OS X users are not affected.
MW works the best for broadband users. If you only have dial-up access, you will probably need to pre-install all models and activities beforehand (use the "Option>Prefetch to Cache" menu from the Molecular Workbench 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.
The most likely issue is that your school has set up a security system that is preventing you from either installing or running the software. See the questions regarding Web Start, proxies, filters, and user access to see if your tech coordinator can help you get the software running.
If you have internet content filtering software, it may be filtering out certain files needed by MW to function properly. The filtering software should allow all files from "concord.org" to be downloaded. If your filtering software filters out types of files by their file extensions, you need to allow the following file types to pass through: gz, mdd, jms, mml, gbl, cml, mws, pdb, xyz, jpg, gif, png, jar, swf, htm, html, txt, mov, rm, and jnlp.
If you need to install Java, then you will probably need Administrative level access to your machine. In some schools, user access to software installation is limited. You may have to get the assistance of your local tech person initially to install the software. Once the software is installed, any user should be able to run it.
In the most restrictive environments, however, where very little 'write access' to the hard drive is allowed, you may have difficulties running Java Web Start and/or MW. Both pieces of software cache some files on the local hard drive (normal for many applications. They write preference information, store local versions of online files, etc. In the case of Web Start, that is one of its core functions: you can run local versions of previously launched java applications.)
Like a browser, MW needs to cache some files to certain directory under the user's own folder. You may not be able to run the software if your system administrator does not permit you to write any data on the hard drive at all. Consult your tech person for this.
This is a bug of earlier Java versions. It occurs when there is a new update of MW. It seems to happen much more frequently on the Windows operating systems than on the Mac OS X systems.
The fix is to download the latest Java software from http://java.com (for Windows and Linux users), or from Apple (for Mac OS X users, the current latest version is J2SE 5.0 Release 3).
If you cannot install software on the machine, the workaround is to remove the previous cache and click the JNLP file again. There are two ways to remove the previously cached MW stuff.
Select "Molecular Workbench" from the table (whether it is in the "User" tab or in the "System" tab), and hit the "Remove Selected Application" button on the lower-left corner of the dialog window. The cached version of Molecular Workbench will be removed.
C:\Documents and Settings\"your user name"\Application Data\Sun\Java\Deployment\cache\javaws\http\Dmw.concord.org. Please remove the entire folder, and try again. If that still doesn't work, remove the following file in the parent directory:
C:\Documents and Settings\"your user name"\Application Data\Sun\Java\Deployment\cache\javaws\lastAccessed
Please follow these steps to make it work:
Currently, only Chinese version for the user interface is provided. For those whose regional setting is China, MW will automatically launch with menus and buttons shown in the corresponding Chinese characters. A limited Russian version is also available.
The limited non-English language support for the user interface does not mean that you cannot write in your language in MW's word processor. Currently, these languages are supported by MW: Arabic (ISO-8859-6), Baltic (ISO-8859-4), Central European (ISO-8859-2), Chinese Simplified (GB18030), Chinese Traditional (Big5), Cyrillic (ISO-8859-5), Greek (ISO-8859-7), Hebrew (ISO-8859-8), Japanese (EUC-JP), Korean (EUC-KR), Thai (ISO-8859-11), Turkish (ISO-8859-9), Western (ISO-8859-1) and Unicode (UTF-8). This means that you can create MW pages in the above languages (if you use Unicode, in any language). For the readers, this is similar to using an English browser to browse non-English Web pages.
Make sure that your Java version is at least 1.5. If not, please go to java.com to download the latest. (Mac OS X users please update your Java software.)
The .cml extension happens to be the same with the Chemical Markup Language's abbreviation. We apologize to our users for the confusion, and to the designers of the Chemical Markup Language for this mistake. We were totally not aware of the Chemical Markup Language at the time when we chose this extension name that was originally an abbreviation of Concord Modeling Language. We do have a plan to change it in the future.