Ensemble PDB instead of .dcd for MD analysis ?

[Former user]

I am trying to run a network analysis of my MD simulation but the processing time is too long on my local computer.

Instead of using a .dcd file is it possible to generate an ensemble PDB of individual frames and then run a network analysis? The rational for doing so would be to decrease the file size of the original input.

[Xinqiu Yao]

I don't think it will decrease the file size or speed up the calculation if you convert a binary trajectory into PDB files. Actually, it is the opposite.

The easiest way is to reduce the number of frames to analyze. You can do it either directly in R, or pre-processing your trajectory files using e.g. AmberTools (if you ran simulation with Amber) or VMD.

[Barry Grant]

Not a bug or issue. Suggest using NetCDF format trajectories or simply reduce the number of frames.

We will be developing new features to better cope with large trajectories in a future package version.