From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon May 21 2012 - 11:34:17 CDT
Yes. You can apply TMD separately to multiple domains simultaneously in a simulation. This is useful, e.g., for creating restraints on internal intradomain motions while allowing interdomain flexibility.
On May 21, 2012, at 10:00 AM, Payne, Christy wrote:
> 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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