VMD-L Mailing List
From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Mon Oct 03 2022 - 13:50:17 CDT
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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!
- Next message: Axel Kohlmeyer: "Re: Overriding default bond heuristics"
- Previous message: Raman Preet Singh: "Overriding default bond heuristics"
- Next in thread: Ashar Malik: "Re: Maximum Stride Possible for Publishable Results"
- Reply: Ashar Malik: "Re: Maximum Stride Possible for Publishable Results"
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