What are the units for mode frequencies in Bio3dNMA?

[Manolo Plasencia]

What are the units for mode frequencies used in Bio3D.NMA, and do these describe the timescale of fluctuation? I assumed wavenumbers based on magnitudes and what I expect for timescales of protein motion, but have yet to find a verbose description in literature.

[Lars Skjærven]

10 THz (10/ps) - should perhaps be updated to THz in next major revison. It's currently not in THz to stay in code consistency with MMTK - in which bio3d nma is largely inspired by. For your question on the timescales, I would point you to a few of Konrad's publications. See e.g. the intro of Analysis of domain motions by approximate normal mode calculations. He summarizes here that * ... the corresponding vibrational frequencies obtained by normal mode analysis are of little physical relevance, because the real frequencies are strongly influenced by anharmonic effects and solvent damping., and * ... the assignment of time scales and amplitudes to these motions requires a detailed model that incorporates anharmonic and solvent effects. . Note that, despite these clear limitations of NMA, the mode directions shows large similarities to both known (e.g. by xray) conformational changes, and also motions extracted from long and detailed MD simulations. Hope this helps. L

[Lars Skjærven]

update frequencies output to THz in next release

[Sebastian S]

Hi, is it currently THz or 10Thz?

[Lars Skjærven]

No changes were done in v2.3 here. Should be updated as we move towards bio3d v3.0.

[Lars Skjærven]

consider updating to Thz in v3.0. keep consistent units for bio3d v2.x