I have been trying to install OpenMM Zephyr by folowing the instructions on p. 15 of your manual. Section 2.3.2.1 says "Save the installation program to your computer and then double click to run the installer." I saved the program to my desktop, where the icon is called "download" and named download.php. But when I double click to run it, I get only a NotePad screen with a lot of characters on it.
Can you help me?
Solution: So I changed the file name to download.exe and clicked on the renamed file. And it proceeded to install OpenMM Zephyr, just as promised in the manual.
I also checked to make sure the installed Zephyr works, and it does.