VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 07 2022 - 16:19:31 CDT

Christos, can you let the VMD team know (either here or directly to them at
vmd_at_ks.uiuc.edu) what changes specifically you didn't like in 1.9.4 on
"another device"? If the device was an Apple machine, you may be likely to
experience issues that are ultimately caused by macOS itself (there were
numerous discussions about this). The Windows builds are generally okay.

Giacomo

On Fri, Oct 7, 2022 at 2:42 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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 $fp
>>
>> Please let me know if there is anything I can do to solve this crashing
>> issue.
>> ------------------------------
>> *From:* Ashar Malik <asharjm_at_gmail.com>
>> *Sent:* Tuesday, October 4, 2022 7:47 AM
>> *To:* Efthymiou, Christos <christos.dereschuk.20_at_ucl.ac.uk>
>> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
>> *Subject:* Re: vmd-l: Maximum Stride Possible for Publishable Results
>>
>>
>> ⚠ Caution: External sender
>>
>> Please share some more details about the hardware you are using for this
>> work (RAM?).
>>
>> Additionally what command did you use to desolvate the protein?
>>
>> Previously I have used catdcd to desolvate entire trajectories and have
>> never had issues.
>>
>> Perhaps if you share more, someone here might be able to figure
>> something out.
>>
>>
>>
>> On Tue, Oct 4, 2022 at 3:28 AM Efthymiou, Christos <
>> christos.dereschuk.20_at_ucl.ac.uk> wrote:
>>
>> Hi,
>>
>> I have run some 100 ns simulations and I would like to analyze them with
>> VMD/QwikMD. However, each MD.dcd file is around 45 GB and causes VMD to
>> crash. I have tried using catdcd to remove the water molecules with a
>> stride of 10, but even after running for several hours it does not finish
>> creating the modified file. Is there a maximum stride value that is
>> reasonable for analyzing simulations? I am concerned about setting a stride
>> value that is too high and then the results not being reliable or as
>> detailed as necessary, but I cannot find any information regarding a
>> consensus or a reasonable range of stride values for analysis.
>>
>> I am also open to any suggestions for analyzing larger simulation files
>> in VMD/QwikMD. Thank you for any input!
>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!7h7MZqHpxXBhkpFux7clGoUsPuyLW2ZLIbhzQhWMauTAs4mEOsR5f8Gk43sPdYzkoP67sWvNVIv_kAZoJhHJmodt8g$
>> <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=http*3A*2F*2Fgoo.gl*2F1wk0&data=05*7C01*7Cchristos.dereschuk.20*40ucl.ac.uk*7Caa511bf23bd34ab2dd6a08daa709c7c8*7C1faf88fea9984c5b93c9210a11d9a5c2*7C0*7C0*7C638005957692304597*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=er*2BM7oW6rO7x*2FYbkReTrwriOXDQN6LrDKRF9b2Q0NeU*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!DZ3fjg!7h7MZqHpxXBhkpFux7clGoUsPuyLW2ZLIbhzQhWMauTAs4mEOsR5f8Gk43sPdYzkoP67sWvNVIv_kAZoJhFHOY9wBw$ >
>> 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!7h7MZqHpxXBhkpFux7clGoUsPuyLW2ZLIbhzQhWMauTAs4mEOsR5f8Gk43sPdYzkoP67sWvNVIv_kAZoJhHJmodt8g$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>