VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 06 2024 - 10:46:16 CST

The VMD installation instructions clearly describe how you can customize
the installation by changing both the path to the installation location and
the name and location of the vmd launch script (i *never* install VMD into
/usr/local but always into $HOME/.local and I sometimes use multiple vmd
executables called vmd_old, vmd_new, vmd_alpha etc.).

All you need to do is carefully and correctly follow the instructions.

On Tue, Feb 6, 2024 at 10:37 AM He, Xibing <xibing.he_at_pitt.edu> wrote:

> Hi Axel and dear all,
>
> The first two issues in my first emails only have minor impacts when
> restarting the computer. All other programs including those with graphic
> user interfaces work fine, including gnuplot, gimp, Maestro (Schrodinger
> Suite), etc., except for VMD. So VMD is the only one which brings trouble
> now.
>
> Yes, it seems that VMD fails to look for something along the paths. That's
> why I look for help from your VMD programmers. Or, if you may guide me to
> compile another executable VMD under my home directory instead of the
> default /usr/local/bin, it would be very helpful!
>
> Regards,
>
> Xibing He, Ph.D.
> Research Scientist
> Department of Pharmaceutical Sciences
> School of Pharmacy
> University of Pittsburgh
> ------------------------------
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Sent:* Monday, February 5, 2024 8:26 PM
> *To:* He, Xibing <xibing.he_at_pitt.edu>
> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: unable to open VMD as normal
>
> Something seems to be messed up with your paths or similar.
> But since your machine is in a bad shape altogether, it is impossible to
> debug and fix this from remote.
>
> On Mon, Feb 5, 2024 at 7:11 PM He, Xibing <xibing.he_at_pitt.edu> wrote:
>
> Hi Axel,
>
> Thanks for your reply!
>
> I do have .vmdrc file under my home directory, but it already contains
> "menu main on" and "menu graphics on". Previously the main window and the
> graphic window would pop out automatically, but not any more now.
>
> I just deleted the ~/.vmdrc file, and typed vmd. Again, only the OpenGL
> Display window appeared, and the text message got stuck there after showing:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
>
> Regards,
>
> Xibing He, Ph.D.
> Research Scientist
> Department of Pharmaceutical Sciences
> School of Pharmacy
> University of Pittsburgh
> ------------------------------
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Sent:* Monday, February 5, 2024 5:58 PM
> *To:* He, Xibing <xibing.he_at_pitt.edu>
> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: unable to open VMD as normal
>
> What you describe about your system suggests that it is not completely
> repaired.
> Only a local person can help you with that.
>
> The situation of having the OpenGL window but not the main VMD window can
> happen, when you have a .vmdrc file in your home directory but it does not
> include the command "menu main on" or there is an error when processing the
> file *before* it reaches the "menu main on" command.
>
> Again, this is something local and usually self-inflicted.
>
> On Mon, Feb 5, 2024 at 1:16 PM He, Xibing <xibing.he_at_pitt.edu> wrote:
>
> Dear all,
>
> Previously I had been running VMD smoothly on my Linux desktop (CentOS7)
> before the mother board and the power supply of the computer were replaced
> with the exact same models as the old ones.
>
> After replacing the mother board and the power supply, my Linux desktop
> have several weird behaviors including failure of starting VMD:
> (1) It cannot be rebooted to the normal login interface unless I choose
> the 2nd Linux core at the beginning process.
> (2) It cannot find the inserted data hard drives. I have to unplug the
> data hard drives, then start the computer, then manually insert the hard
> drives one at each time and type commands to mount the hard drives one by
> one.
> (3) When I type 'vmd', only the VMD OpenGL Display window is popped out,
> but the "main" window never appears. It seems that VMD is hanging there and
> waiting for something forever. The text messages on the terminal is as
> follows:
>
> [xibing_at_qin ~]$ which vmd
> /usr/local/bin/vmd
> [xibing_at_qin ~]$ vmd
> Info) VMD for LINUXAMD64, version 1.9.4a57 (April 27, 2022)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 64 CPUs.
> Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
> Info) Free system memory: 231GB (91%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator::
> Info) [0] GeForce GTX 1080 Ti 28 SM_6.1 1.6 GHz, 11GB RAM SP32 KT AE2 ZC
> Info) OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture
> (4)
> Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> Info) Compiling OptiX shaders on 1 target GPU...
> Info) Dynamically loaded 3 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl /home2/xibing/scripts/vmd/la1.0
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl /home2/xibing/scripts/vmd/la1.0
> /home2/xibing/scripts/vmd/orient
>
> Can anyone help me figure out the reason behind? We can schedule a Zoom
> meeting so that you may access to my Linux desktop remotely.
>
> Thanks!
>
> Xibing He, Ph.D.
> Research Scientist
> Department of Pharmaceutical Sciences
> School of Pharmacy
> University of Pittsburgh
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__https://goo.gl/1wk0__;!!DZ3fjg!8QC9KTcp3gXqAWgKbBGghRJ7_x2gy3SijvXD16CI_t1oCVSOJtlHRvvHhRz8IHldQ5rspf_YdWcCZjGpXw$
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> Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!8QC9KTcp3gXqAWgKbBGghRJ7_x2gy3SijvXD16CI_t1oCVSOJtlHRvvHhRz8IHldQ5rspf_YdWcVem6cYA$
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>
> College of Science & Technology, Temple University, Philadelphia PA, USA
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__https://goo.gl/1wk0__;!!DZ3fjg!8QC9KTcp3gXqAWgKbBGghRJ7_x2gy3SijvXD16CI_t1oCVSOJtlHRvvHhRz8IHldQ5rspf_YdWcCZjGpXw$
> Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!8QC9KTcp3gXqAWgKbBGghRJ7_x2gy3SijvXD16CI_t1oCVSOJtlHRvvHhRz8IHldQ5rspf_YdWcVem6cYA$
>
> College of Science & Technology, Temple University, Philadelphia PA, USA
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__https://goo.gl/1wk0__;!!DZ3fjg!8QC9KTcp3gXqAWgKbBGghRJ7_x2gy3SijvXD16CI_t1oCVSOJtlHRvvHhRz8IHldQ5rspf_YdWcCZjGpXw$ 
Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!8QC9KTcp3gXqAWgKbBGghRJ7_x2gy3SijvXD16CI_t1oCVSOJtlHRvvHhRz8IHldQ5rspf_YdWcVem6cYA$ 
College of Science & Technology, Temple University, Philadelphia PA, USA