From: Efthymiou, Christos (
Date: Thu Feb 02 2023 - 17:45:36 CST


I am trying to use the CaFE plugin on a trajectory, but I have noticed that when I set the stride value in the CaFE script it appears to only apply to when the new trajectory is generated. For example, the following gets printed in the console after starting the script:

CaFE) Sanity check
CaFE) Found 5508 atoms for complex
CaFE) Found 4646 atoms for receptor
CaFE) Found 862 atoms for ligand
CaFE) Loaded 10000 frames for complex
CaFE) Generating new trajectory for complex
CaFE) Loaded 10 frames for complex

Therefore, it appears that the full trajectory from the -trj command is loaded, and then the -stride command is only taken into account when generating the new trajectory to perform the analysis. However, I have much larger trajectories that I would like analyze with CaFE and I cannot load the full trajectory into VMD at one time or it takes an extremely long time and would like to set a stride. Is it possible to set a stride value for the initial trajectory when using CaFE?