I have my final trajectory file and would like to use it for Structural DNA Helical Parameters. However, the file is larger than 500 MB and I am looking for recommendations on how to reduce the size of the file.
Dear Aleique Allen,
I assume you are using the BioBB-wfs web server (and thus the 500MB limitation). Remember you can also try to install the workflow in your own computer, with jupyter notebooks or pure Python.
If you are just interested in the helical parameters, you can reduce the trajectory with just selecting a number of snapshots from the original one representing the full simulation. For example, taking one snapshot every 10ps or 100ps (that’s what we used in our BigNASim database). This should not affect much the final result, and can be easily done with any of the available MD analysis packages (pytraj, mdanalysis, mdtraj, etc.) and also with our BioBB library (cpptraj_slice).
Hope this helps!
Regards,
-Adam-