From: He, Xibing (
Date: Mon Feb 05 2024 - 17:35:11 CST

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


Xibing He, Ph.D.
Research Scientist
Department of Pharmaceutical Sciences
School of Pharmacy
University of Pittsburgh
From: Axel Kohlmeyer <>
Sent: Monday, February 5, 2024 5:58 PM
To: He, Xibing <>
Cc: <>
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 <<>> 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
[xibing_at_qin ~]$ vmd
Info) VMD for LINUXAMD64, version 1.9.4a57 (April 27, 2022)
Info) Email questions and bug reports to<>
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) 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.


Xibing He, Ph.D.
Research Scientist
Department of Pharmaceutical Sciences
School of Pharmacy
University of Pittsburgh

Dr. Axel Kohlmeyer<>;!!DZ3fjg!6njjz3RV1lMGgMDPwKR-uIbN-XzSw1_eMUo-GmB474uSx9Ng9esiCUQ8QGzuReJ-tVhH3V0D33ikDjP4i8xj0Q$ 
Institute for Computational Molecular Science and HPC,;!!DZ3fjg!6njjz3RV1lMGgMDPwKR-uIbN-XzSw1_eMUo-GmB474uSx9Ng9esiCUQ8QGzuReJ-tVhH3V0D33ikDjPSYm9kzA$ <;!!DZ3fjg!6njjz3RV1lMGgMDPwKR-uIbN-XzSw1_eMUo-GmB474uSx9Ng9esiCUQ8QGzuReJ-tVhH3V0D33ikDjPZNg1x8A$ >
College of Science & Technology, Temple University, Philadelphia PA, USA