VMD-L Mailing List

From: Corenflos, Steven (scorenfl_at_indiana.edu)
Date: Wed Dec 22 2010 - 15:57:58 CST

The researchers in my lab are attempting to use the VMD 1.8.7 64-bit binary on an Ubuntu Linux 8.04 server. They connect to it via ssh with X-forwarding. They can't do it on their desktops because the high-atom systems they're modeling require the extra RAM of the server.

I understand this is sub-optimal as that's a lot of information to send over the network but I'm not sure there's a better way to do it locally but using the resources of the remote machine. Any suggestions there would be appreciated.

Unfortunately lately we've been getting errors and VMD seems unable to render what they need. The VMD window opens but is blank. Below is a sample of the output from VMD. Searching the mailing list I found one instance of these errors before and it said that it *may* be related to problems with the X server but I wasn't clear about the appropriate solution if that is the case.

Any help would be greatly appreciated!

Thanks,
-Steve

user_at_remoteserver:~/L1$ vmd L1.pdb
rlwrap: Command not found.
Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
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, 8 CPUs detected.
Info) Free system memory: 15173MB (94%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Quadro NVS 290/PCI/SSE2
Info) Features: STENCIL MDE MTX NPOT PP PS
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
Info) File loading in progress, please wait.
Info) Using plugin pdb for structure file L1.pdb
Info) Using plugin pdb for coordinates from file L1.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file L1.pdb.
Info) Analyzing structure ...
Info) Atoms: 7075
Info) Bonds: 7171
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 455
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
XRequest.135: BadLength (poly request too large or internal Xlib length error) 0x5400091
XRequest.135: GLXBadLargeRequest 0x2
XRequest.135: BadLength (poly request too large or internal Xlib length error) 0x2
XRequest.135: GLXBadLargeRequest 0x2
XRequest.135: BadLength (poly request too large or internal Xlib length error) 0x2
XRequest.135: BadLength (poly request too large or internal Xlib length error) 0x2
XRequest.135: GLXBadLargeRequest 0x2