From: Lee-Ping Wang (
Date: Fri Sep 11 2015 - 04:35:12 CDT

Hi everyone,

I've recently encountered a problem where VMD will crash when loading a rather large trajectory file (.xyz format, 700 MB, 44 atoms, 293360 frames). The error message is attached at the end of this email. This happens on a new Mac laptop that I recently purchased with 16 GB of memory with no other programs running.

I'm puzzled because my previous Mac laptop with 8 GB of memory was able to load a trajectory of this size with no issues. The "activity monitor" reports a small amount of memory used (about 1 GB allocated to VMD) when this crash occurs. I confirmed this error still happens with VMD 1.9.1, which is the version I had on my previous laptop.

If anyone could help me troubleshoot, I'd greatly appreciate it.

Thanks a lot,

- Lee-Ping

leeping_at_campus-003-211:~/projects/LPW07-Acetone/Dimer/rhf-631gs/Consolidated$ vmd

Info) VMD for MACOSXX86, 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, 8 CPUs detected.

Info) OpenGL renderer: ATI Radeon R9 M370X OpenGL Engine


Info) Full GLSL rendering mode is available.

Info) Textures: 2-D (16384x16384), 3-D (16384x16384x16384), Multitexture (8)

Info) Dynamically loaded 2 plugins in directory:

Info) /Applications/VMD

Info) File loading in progress, please wait.

Info) Using plugin xyz for structure file

Info) Using plugin xyz for coordinates from file

Info) Determining bond structure from distance search ...

vmd_MACOSXX86(61772,0xa0f2f1d4) malloc: *** mach_vm_map(size=8388608) failed (error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

Segmentation fault: 11 (core dumped)