The only way that your systems would be running the same protein is if they are calling from the same directory.
See post 52 and post 89 from ken from texas.
Here is a note from the F@H FAQs:
Does Folding@home run on dual processor machines? Yes, you can. Additional processors must run the console version (with the "-local" command-line argument if run on Windows). First, make additional directories for each processor and copy the FAH Console executable file into each. Then configure them with the -config switch, filling in settings for each. It is very important to make sure that under the "Advanced Settings" option each copy is given a unique machine ID (from 1 to 8). The first copy will default to a machine ID of 1, so additional copies should be given IDs of 2, 3, 4, etc. Each may then be run out of their installed directory, using the -local switch on windows.
Is there anything special I should do to run on a cluster? The main aspect to consider is to make sure that the CPUID for each machine is unique. To help fight from having duplicate IDs, the windows versions (v. 3 and later) keep their IDs in the registry and the Linux version (v. 3.11 and later) keep it in a special file MachineDependent.dat.
Ways to avoid duplicating IDs:
If you install each client individually, then it's impossible for there to be problem with a duplicate ID.
If you use the recent Windows version and have single processor machines, then you should also be fine (for duals, see the above).
For a Linux cluster, make sure that if you copy the directory, you DON'T copy the MachineDependent.dat file. This file will be auto generated by the client to get a new ID.
Can I download more than one unit at a time? The algorithm we use works best if everybody downloads one work unit at a time, and checks back after each unit is completed, so therefore there is no option to download multiple units. If you have multiple processors in your computer, it is possible to have each processor work on a different unit; see what to do here. Don't try to run two copies on different machines that use the same directory on the same filesystem, either-- they NEED to run in different directories.
Clear as mud? Sorry about that. The net rsult is that each instance of F@H running on a multiprocessor system will need its own directory and its own unique machine ID.
Okay, I uninstalled both programs and paid more closely to the installation process.
It seems that upon installation, the console program looks for a preexisting work folder in the registry keys (which the GUI version installs). So, that's where the conflict was coming from.
Crossing my fingers now.