From: Matic Kisovec (
Date: Fri May 15 2015 - 10:53:33 CDT

Hi Justin,

I am not an expert on virtualization but I do use it daily at work.
I use Ubuntu as host OS and Windows as guest inside Virtualbox. In my experience the performance is usually (considerably/in many cases) worse inside VM. My experience is that when it comes to graphics inside VM it is even worse. It is just my point of view and I am not saying it is always like that (and it really shouldn't be!).

I am not familiar with WMWare and also rarely used Windows (only tested once or twice) a host.
Since you already invested some time in this I sure hope you get some help on this list.

My advice would be (if circumstances allow of course) to do a dual boot setup on your machine. It is an investment in time but again I believe it is worth it in the long run. If you have enough hard disk space and sufficient administrator rights on your machine you should be OK. It is mandatory to be careful when resizing partitions and never do that without a backup! I rather do a dual boot on a second HDD (perhaps you have some old PCs laying around with working HDD that you can safely format) and then use this for linux without even touching the Windows partition.

You may have your reasons to use VM and in that case I hope you will be able to get some advice from VMD community.

All the best,

On 15. 05. 2015 11:16, Justin wrote:
The VMD for Windows has only the 32-bit version and this is incapable of handling larger trajectories, it normally crashes when I try to load a larger trajectory (>1GB).

So I have tried running VMD 64-bit for Linux in a virtual machine on VMWare 7.1.0. The guest OS is CentOS 7.1 64-bit and the host OS is Windows 8.1 64-bit.

Unfortunately the performance is quite poor. Using render mode Normal, it is very slow to rotate and move the protein structure around using the NewCartoon drawing method. Surprisingly it is very smooth when I change the render mode to Acrobat3D. GLSL rendering displays a weird red pentagon with a circle in the middle regardless of drawing method. CPK drawing mode is extremely slow for both Normal and Acrobat3D. Lines drawing method is slow but bearable for both Normal and Acrobat3D rendering modes

I have checked VMWare and made sure that I have enabled CPU hardware acceleration and 3D hardware acceleration on VMWare and installed installed VMWare Tools. To ensure the 3D hardware acceleration support through OpenGL in Linux, I have built the vmwgfx, xf86-video-vmware, Mesa/gallium OpenGL driver svga and user-space libdrm library by following the guide at

Running: "glxinfo | grep OpenGL". I get:

OpenGL vendor string: VMware, Inc.
OpenGL renderer string: Gallium 0.4 on SVGA3D; build: RELEASE;
OpenGL version string: 2.1 Mesa 10.6.0-devel (git-4ab8d59)
OpenGL shading language version string: 1.20
OpenGL extensions:

Running VMD I get:
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
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, 4 CPUs detected.
Info) Free system memory: 12833MB (96%)
Warning) Detected a mismatch between CUDA runtime and GPU driver
Warning) Check to make sure that GPU drivers are up to date.
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this X server option. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: Gallium 0.4 on SVGA3D; build: RELEASE;
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile

I also ran Microsoft Sysinternals Suite's Process Explorer to monitor the GPU usage while running VMD in VMWare and I do indeed find VMWare using the GPU although the % utilization is quite low ~7-10%.

Is there anything else that I can do to improve the performance of VMD in the VM?
More specifically, is there a way to get VMD/Linux/VMWare to make better use of my GPU on Windows?

Thanks in advance.