From: Kliuchnikov, Evgenii (
Date: Mon Sep 16 2019 - 20:59:47 CDT


The problem was that one of the coordinates was nan, so VMD was not able to load this structure.

Thank you for your response,
От: John Stone <>
Отправлено: 16 сентября 2019 г. 21:07
Кому: Kliuchnikov, Evgenii <>
Копия: Miro Astore <>; <>
Тема: Re: vmd-l: VMD segmentation fault (core dumped)

  It looks to me like VMD might be crashing during bond determination.
What program generated the DCD file you're loading? Are you certain that
your coordinates are in the right units? Do you have an associated PSF
file to go with the PDB? Why are you converting the DCD file into a PDB?
There may be trouble in the conversion you've done there. What program
generated the PDB?

  John Stone

On Mon, Sep 16, 2019 at 10:51:16PM +0000, Kliuchnikov, Evgenii wrote:
> I guess there is no useful information, but
> Info) VMD for LINUXAMD64, version 1.9.4a29 (February 25, 2019)
> Info);!vt9fxkjPvaI!Oc_si53Zmu_wMBkmr5spE19JixqlqZEuYTbxYwDomVNoEqyhrgaFeNZKZSm3jTk2XNihMrlQxBgHkYQ$
> 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, 12 CPUs detected.
> Info) CPU features: SSE2 AVX AVX2 FMA
> Info) Free system memory: 19GB (60%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] GeForce GTX 1060 6GB 10 SM_6.1 1.84 GHz, 5.9GB RAM, KTO, AE2,
> 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: GeForce GTX 1060 6GB/PCIe/SSE2
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture
> (4)
> Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> Info) Compiling 1 OptiX shaders on 1 target GPU...
> Info) Dynamically loaded 3 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin pdb for structure file last_frame.pdb
> Info) Using plugin pdb for coordinates from file last_frame.pdb
> Info) Determining bond structure from distance search ...
> Segmentation fault (core dumped)
> --------------------------------------------------------------------------
> Ot: Miro Astore <>
> Otpravleno: 16 sentyabrya 2019 g. 18:44
> Komu: Kliuchnikov, Evgenii <>
> Kopiya: <>
> Tema: Re: vmd-l: VMD segmentation fault (core dumped)
> Hi, can you post the full error message?
> On Tue, 17 Sep 2019 at 04:17, Kliuchnikov, Evgenii
> <[1]> wrote:
> Hello VMD users,
> I have pdb-file and dcd-trajectory that can be loaded into that pdb.
> After that I save last frame of this trajectory, but when I try to load
> this last frame in vmd it gives me segmentation fault error. What could
> be the problem?
> Sincerely,
> Evgenii
> References
> Visible links
> 1.

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