VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Oct 03 2022 - 23:47:24 CDT

Please share some more details about the hardware you are using for this
work (RAM?).

Additionally what command did you use to desolvate the protein?

Previously I have used catdcd to desolvate entire trajectories and have
never had issues.

Perhaps if you share more, someone here might be able to figure
something out.

On Tue, Oct 4, 2022 at 3:28 AM Efthymiou, Christos <
christos.dereschuk.20_at_ucl.ac.uk> wrote:

> 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!
>
>
>