From: fabio trovato (
Date: Sat Nov 02 2019 - 11:03:40 CDT


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) 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.
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.