VMD-L Mailing List

From: Efthymiou, Christos (christos.dereschuk.20_at_ucl.ac.uk)
Date: Wed Oct 05 2022 - 13:30:00 CDT

Is it possible to download VMD 1.9.4 while keeping 1.9.3 functioning as well? I had tried 1.9.4 on another device, and there were some changes made I did not particularly like, so I want to be able to use both versions if possible.
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From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Tuesday, October 4, 2022 9:31 PM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
Cc: Ashar Malik <asharjm_at_gmail.com>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Maximum Stride Possible for Publishable Results

VMD 1.9.3 is old, and the 1.9.4 alpha releases are rather mature now.

Second, the Windows build for 1.9.3 specifically is a 32-bit executable, so you are limited in file size (whether 2 GB or 4 GB I don't remember). 1.9.4 has 64-bit builds available; you should be able to read in your file, provided you use a stride >> 1 to avoid filling up your system RAM with the DCD file's contents.

Giacomo

On Tue, Oct 4, 2022 at 2:22 PM Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk<mailto:christos.dereschuk.20_at_ucl.ac.uk>> wrote:
I am using VMD 1.9.3 on a Windows 10 computer with 32 GB of RAM.

The command I used for catdcd was: catdcd -o MD_protein.dcd -otype dcd -i indexfile -dcd MD.dcd.

To create the index file, I loaded my PSF and PDB file into VMD and then ran this script from the TK console:

set fp [open indexfile w]
set a [atomselect top "protein"]
puts $fp [$a get index] nonewline
$a delete
close $fp

Please let me know if there is anything I can do to solve this crashing issue.
________________________________
From: Ashar Malik <asharjm_at_gmail.com<mailto:asharjm_at_gmail.com>>
Sent: Tuesday, October 4, 2022 7:47 AM
To: Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk<mailto:christos.dereschuk.20_at_ucl.ac.uk>>
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: Re: vmd-l: Maximum Stride Possible for Publishable Results


⚠ Caution: External sender

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<mailto: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!