They point out that only running NMA on alpha carbons might be insufficient, but I think that's because they're actually generating force fields and stuff. Since we already have trajectories from a full MD, it feels like we should have accurate results.
It'll be very useful to run both types and compare, making sure to use our trajectories rather than bio3d's MD.
"Example 2: All-atom normal mode analysis (ENM)" contains instructions on running normal mode analysis in bio3d in different ways: http://thegrantlab.org/bio3d_v2/tutorials/normal-mode-analysis
They point out that only running NMA on alpha carbons might be insufficient, but I think that's because they're actually generating force fields and stuff. Since we already have trajectories from a full MD, it feels like we should have accurate results.
It'll be very useful to run both types and compare, making sure to use our trajectories rather than bio3d's MD.