TMD output format

From: Payne, Christy (
Date: Mon May 21 2012 - 10:00:24 CDT

I have question regarding the output format from the TMD application. I get output like this from the TMD runs.

TMD 0 Domain: 0 2.44195e-05 2.44195e-05
TMD 10 Domain: 0 2.44195e-05 0.0998741
TMD 20 Domain: 0 2.44194e-05 0.149118
TMD 30 Domain: 0 2.44194e-05 0.182621
TMD 40 Domain: 0 2.44193e-05 0.232706

The NAMD UG says this about the output. "TMD output consists of lines of the form TMD ts targetRMS currentRMS
where ts is the timestep, targetRMS is the target RMSD at that timestep, and currentRMS
is the actual RMSD."

My confusion arises from the presence of the "Domain: 0" portion of the output. Is that just an index of the domain to which the force is applied? So if I had two domains, there would be "Domain: 0" and "Domain: 1" output lines? And for clarification, the last value in this output format is still the currentRMS value?

Thanks so much for the clarification!

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