NMA on Larger Molecules

[jmcavity]

Hi, we are attempting to compute the NMA of arrestin structures (e.g., PDB code 1JSY), each of which have around 3,000 atoms. We were able to make the code work on the provided water examples, but are having difficulty with larger molecules. In the resultant trajectories, a very small subset of the molecule seems to move significantly, while the rest of the molecule appears to be rigid. This makes us think that the code may only be looking at that small subset, but we have been unable to determine why this might be the case or if there is a different problem we’re not seeing. We would greatly appreciate some insight!