From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Mon Oct 03 2022 - 13:50:17 CDT

Hi,

I have run some 100 ns simulations and I would like to analyze them with VMD/QwikMD. However, each MD.dcd file is around 45 GB and causes VMD to crash. I have tried using catdcd to remove the water molecules with a stride of 10, but even after running for several hours it does not finish creating the modified file. Is there a maximum stride value that is reasonable for analyzing simulations? I am concerned about setting a stride value that is too high and then the results not being reliable or as detailed as necessary, but I cannot find any information regarding a consensus or a reasonable range of stride values for analysis.

I am also open to any suggestions for analyzing larger simulation files in VMD/QwikMD. Thank you for any input!