From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Oct 07 2022 - 13:42:45 CDT

You need to be using Linux to be able to do what I suggested. I never used
VMD on Windows and rarely use Windows anyway, so I don't know what your
options there are.
Axel.

On Fri, Oct 7, 2022 at 2:34 PM Efthymiou, Christos <
christos.dereschuk.20_at_ucl.ac.uk> wrote:

> Hi,
>
> I am not sure I understand how to install the two versions into different
> folders. I went to the VMD 1.9.4 download page and downloaded the .exe file
> for VMD 1.9.4a53 for Windows. When I run this file, I am prompted to accept
> the agreement and then the program is installed automatically. I am never
> prompted to select a folder/path for where I want the new version
> installed. If I go to Apps and Features, the option to "Modify" the program
> is greyed out so I cannot move it to another folder after installation. It
> has written over some of the files in my VMD 1.9.3 folder, so I am not sure
> what to do.
>
> Thank you for any advice.
>
> Best,
> Christos
> ------------------------------
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Sent:* Wednesday, October 5, 2022 10:42 PM
> *To:* Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
> *Cc:* Giacomo Fiorin <giacomo.fiorin_at_gmail.com>; 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
>
> You can install both into different folders and also give different names
> to the "vmd" script. Both can be set in the "configure" script before you
> run it. there are plenty of comments.
>
> On Wed, Oct 5, 2022 at 3:06 PM Efthymiou, Christos <
> christos.dereschuk.20_at_ucl.ac.uk> wrote:
>
> 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.
> ------------------------------
> *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> 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 $fp
>
> Please let me know if there is anything I can do to solve this crashing
> issue.
> ------------------------------
> *From:* Ashar Malik <asharjm_at_gmail.com>
> *Sent:* Tuesday, October 4, 2022 7:47 AM
> *To:* Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: Maximum Stride Possible for Publishable Results
>
>
> ⚠ Caution: External sender
>
> Please share some more details about the hardware you are using for this
> work (RAM?).
>
> Additionally what command did you use to desolvate the protein?
>
> Previously I have used catdcd to desolvate entire trajectories and have
> never had issues.
>
> Perhaps if you share more, someone here might be able to figure
> something out.
>
>
>
> On Tue, Oct 4, 2022 at 3:28 AM Efthymiou, Christos <
> christos.dereschuk.20_at_ucl.ac.uk> wrote:
>
> Hi,
>
> I have run some 100 ns simulations and I would like to analyze them with
> VMD/QwikMD. However, each MD.dcd file is around 45 GB and causes VMD to
> crash. I have tried using catdcd to remove the water molecules with a
> stride of 10, but even after running for several hours it does not finish
> creating the modified file. Is there a maximum stride value that is
> reasonable for analyzing simulations? I am concerned about setting a stride
> value that is too high and then the results not being reliable or as
> detailed as necessary, but I cannot find any information regarding a
> consensus or a reasonable range of stride values for analysis.
>
> I am also open to any suggestions for analyzing larger simulation files in
> VMD/QwikMD. Thank you for any input!
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!-6SzQb0o6IsPy0niGNH7Vmid_Q0BdnuHli-gYJF5NVGDhsHaZXFKAAtybKKZVclt85-g4M1CUNqAt413rw$
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> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!-6SzQb0o6IsPy0niGNH7Vmid_Q0BdnuHli-gYJF5NVGDhsHaZXFKAAtybKKZVclt85-g4M1CUNqAt413rw$  
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.