From: John Stone (
Date: Wed Nov 13 2019 - 00:37:10 CST

This looks like a build you did for yourself. Without knowing
precisely what libraries you compiled against it's impossible
to guess what's going wrong there, but there's a 99% chance this
is a problem with the particular FLTK build you're using. It would
be good to know what version you tried since it clearly doesn't
work properly (the ones I've worked on thus far have other issues).

  John Stone

On Sat, Nov 02, 2019 at 05:03:40PM +0100, fabio trovato wrote:
> Hello,
> I have installed the last VMD version, without SURF library (for some
> errors, see previous post). The program starts, I can load a trajectory,
> but the molecule is confined to a small rectangle in the bottom-left
> corner of the main window. If I reset the view, using =, the molecule
> becomes centered in the small rectangle, while I was expecting to be
> centered in the entired main window.
> What can be the problem?
> I have attached also the messages printed in the console upon VMD
> startup.
> vmd start_no_linear_674beads.pdb traj_gpu0_0.dcd
> Info) VMD for MACOSXX86_64, version 1.9.4a38 (November 2, 2019)
> Info) [1]
> Info) Email questions and bug reports to [2]
> 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.
> DEPRECATION WARNING: The system version of Tk is deprecated and may be
> removed in a future release. Please don't rely on it. Set
> TK_SILENCE_DEPRECATION=1 to suppress this warning.
> Info) OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture
> (8)
> Info) File loading in progress, please wait.
> Info) Using plugin pdb for structure file start_no_linear_674beads.pdb
> Info) Using plugin pdb for coordinates from file
> start_no_linear_674beads.pdb
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file start_no_linear_674beads.pdb.
> Info) Analyzing structure ..
> Info) Atoms: 674
> Info) Bonds: 0
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 674
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 674 Protein: 0 Nucleic: 0
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> Info) Using plugin dcd for coordinates from file traj_gpu0_0.dcd
> Info) Finished with coordinate file traj_gpu0_0.dcd.
> References
> Visible links
> 1.
> 2.

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349