VMD-L Mailing List

From: Stefan Boresch (stefan_at_mdy.univie.ac.at)
Date: Mon Jan 04 2021 - 04:23:11 CST

John,

sorry for the late reply!

I finally tested this for 1.9.4a50 (December 17, 2020)

Starting fails both from command.exe as well as powershell, if the
program attempts to initialize OSPRAY. If I use VMDNOOSPRAY=1 then
vmd starts fine/identically from command prompt as well as a powershell
window.

While I know that in my setup some paths etc are different in the two
environment, they have no effect on vmd / the OSPRAY issue.

Belatedly all the best for the New Year!

Stefan

On Thu, Dec 31, 2020 at 12:01:56PM -0600, John Stone wrote:
> Gustavo,
> I noticed that two people have mentioned having trouble when trying
> to run VMD from a Windows Power Shell prompt. What if you run VMD from
> a normal "cmd.exe" window instead?
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Dec 18, 2020 at 02:09:24PM -0300, Gustavo Scheiffer wrote:
> > Hello,
> > I suppose there isn't really a problem with access privileges, since I
> > tried running VMD from an elevated prompt as well. I'm starting to suspect
> > maybe VMD is requesting some Windows service that I disabled in the past
> > (any guesses?). Anyway, I find it quite weird, never had this kind of
> > problem before with any software. Also, I discovered that the same exact
> > message pops-up when I click the installer of the newer 64-bit version.Â
> > In summary: The other versions I can install, but not execute. The 64-bit
> > I can't even install. The same message appears on both cases.
> > Regarding the Ctrl+V suggestion, there wasn't any effect.
> > Best,
> > Gustavo Scheiffer
> > On Tue, Dec 15, 2020, 17:16 Stefan Boresch <[1]stefan_at_mdy.univie.ac.at>
> > wrote:
> >
> > [I fully understand that you are not even getting that far.]
> >
> > However, your earlier message with access issues reminded me of one
> > difference I noticed on Windows (compared to Linux, my normal
> > 'habitat'). Specifically, when vmd is started via the icon (mouse
> > clicking) or through file association (open *.pdb with vmd), your
> > working directory is the install directory, and, e.g., (some) output
> > files (e.g. for rendering) default to that directory, to which you
> > (unless you are running as admin) have no write access. (This might be
> > the case on Linux, too, but there I start vmd practically always via
> > the command line in the directory I plan to work in ..)
> >
> > While I work around this by starting vmd on Windows also from the
> > command line, this is 'fun' to explain to students who see the commandÂ
> > line
> > for the first time.
> >
> > Finally, I have seen vmd hang on Windows on occasion for quite some time
> > (John provided an explanation a few weeks back here). When you get so
> > far that vmd
> > does something in the powershell window, have you tried just hitting
> > 'Enter'
> > and/or Ctrl-C? In most cases, vmd then starts up relatively quickly.
> >
> > Best,
> > Stefan
> >
> > On Tue, Dec 15, 2020 at 04:03:45PM -0300, Gustavo Scheiffer wrote:
> > > Hi,
> > > Yes, I always confirm the administrator privileges pop-up. The
> > installation
> > > itself seems to finish without any problems and there's plenty of disk
> > > space. I tried executing VMD via Powershell to investigate further and
> > > verified that the program seems to quit (maybe crashing?) right after
> > > opening.
> > >
> > > Output from Powershell:
> > >
> > > PS C:\VMD> .\vmd.exe
> > > PS C:\VMD> .\vmd.exe
> > > PS C:\VMD> .\vmd.exe
> > > PS C:\VMD> .\vmd.exe
> > > PS C:\VMD> .\vmd.exe
> > > PS C:\VMD> .\vmd.exe
> > > PS C:\VMD> .\vmd.exe
> > > PS C:\VMD> .\vmd.exe (yes, I needed to execute vmd 8 times to get the
> > > output below)
> > > Info) VMD for WIN32, version 1.9.3 (November 30, 2016)
> > > Info) [2]http://www.ks.uiuc.edu/Research/vmd/
> > > Info) Email questions and bug reports to [3]vmd_at_ks.uiuc.edu
> > > Info) Please include this reference in published work using VMD:
> > > Info)Â Â Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > > Info)Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > > Info) -------------------------------------------------------------
> > > Info) Multithreading available, 4 CPUs detected.
> > > Info) Free system memory: 1075MB (26%)
> > > PS C:\VMD> -- (VMD just stopped here?)
> > >
> > > Worth noting that the warning message mentioned in the previous email
> > only
> > > appears sometimes (sometimes the VMD window just popup for less than a
> > > second). Is there some conflict happening? For the record, I'm using
> > an
> > > Intel HD Graphics 4600 (drivers up to date).
> > >
> > > Em ter., 15 de dez. de 2020 Ã s 03:46, John Stone
> > <[4]johns_at_ks.uiuc.edu>
> > > escreveu:
> > >
> > > > Hi,
> > > >Â Â When you try installing VMD, do you have administrator
> > priveleges?
> > > > Are you out of disk space?
> > > >
> > > > Best,
> > > >Â Â John Stone
> > > >Â Â [5]vmd_at_ks.uiuc.edu
> > > >
> > > > On Sat, Dec 12, 2020 at 04:01:30AM -0300, Gustavo Scheiffer wrote:
> > > > >Â Â Hello,
> > > > >Â Â I just can't manage to make VMD work on my PC (Windows 10). I
> > tried
> > > > many
> > > > >Â Â different versions, alwaysÃ* resulting in the sameÃ* problem.
> > When I
> > > > click
> > > > >Â Â on the VMD.exe, Windows exhibitsÃ* a warning message "Windows
> > cannot
> > > > >Â Â accessÃ* theÃ* specified device,Ã* path, orÃ* file.Ã* You may
> > notÃ* have the
> > > > >Â Â appropriate permissions to access the item". I was really
> > hoping to
> > > > use
> > > > >Â Â VMD to learn NAMD.
> > > > >Â Â Best regards,
> > > > >Â Â Gustavo Scheiffer
> > > >
> > > > --
> > > > NIH Center for Macromolecular Modeling and Bioinformatics
> > > > Beckman Institute for Advanced Science and Technology
> > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > [6]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone:
> > 217-244-3349
> > > > [7]http://www.ks.uiuc.edu/Research/vmd/
> > > >Â
> >
> > References
> >
> > Visible links
> > 1. mailto:stefan_at_mdy.univie.ac.at
> > 2. http://www.ks.uiuc.edu/Research/vmd/
> > 3. mailto:vmd_at_ks.uiuc.edu
> > 4. mailto:johns_at_ks.uiuc.edu
> > 5. mailto:vmd_at_ks.uiuc.edu
> > 6. http://www.ks.uiuc.edu/~johns/
> > 7. http://www.ks.uiuc.edu/Research/vmd/
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>