VMD-L Mailing List

From: Kliuchnikov, Evgenii (Evgenii_Kliuchnikov_at_student.uml.edu)
Date: Mon Sep 16 2019 - 17:51:16 CDT

I guess there is no useful information, but

Info) VMD for LINUXAMD64, version 1.9.4a29 (February 25, 2019)
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, 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, ZCP
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) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
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)
________________________________
От: Miro Astore <miro.astore_at_gmail.com>
Отправлено: 16 сентября 2019 г. 18:44
Кому: Kliuchnikov, Evgenii <Evgenii_Kliuchnikov_at_student.uml.edu>
Копия: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Тема: 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 <Evgenii_Kliuchnikov_at_student.uml.edu<mailto:Evgenii_Kliuchnikov_at_student.uml.edu>> 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