VMD: VMD can be found at this link. Choose the latest version (currently 1.9.4). You must choose your operating system, and register your email address. This is an academic site so your email won’t end up in any spam lists. Install it by following the directions. When you open it for the first time, you will get a warning from OSX that it is from an unknown developer. Open System Preferences -> Security and Privacy, and a box should be there which will allow you to open VMD. You will need to enter your password.
NAMD: NAMD can be found at this link. Again, choose the latest version (2.13). Your email address/password from the VMD step can be used here, also. You should put this in your "Applications" folder and rename the folder "NAMD" (removing everything after the first four characters). Again, you may need to enter your password to move NAMD to Applications.
Packmol: We will use the 'packmol' program later on in the semester. Save it to your home directory.
Files: various files will be listed here, as well as on the sections they are required. In general, these are gzipped archives. Download them to your Projects folder, mentioned above.
(You should be able to access these files individually under the "Files" tab on the right of the page(s), too.)
Students should organize their files. Here is the suggested file structure:
