VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 13 2015 - 16:14:13 CDT

Hi,
  There was a bug in the Gromacs plugin in VMD 1.9.2 that has since
been corrected. The latest code in the VMD CVS fixes the problem.
I hope to post a new set of test builds of VMD 1.9.3 in the next few days,
if you don't want to compile the source yourself.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 14, 2015 at 12:30:30AM +0330, Nima Soltani wrote:
> Hi everyone
> my problem is that almost whenever i want to load a GROMACS trajectory
> (*.trr or *.xtc) or even a Gromacs coordinate file (*.gro) the vmd fails
> and show the following Error at Terminal:
> Segmentation fault (core dump)
> I run VMD with -debug option and after getting the same error i typed
> "where" it gives me the following information:
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00000000007709fd in stringdup(char const*) ()
> (gdb) where
> #0 0x00000000007709fd in stringdup(char const*) ()
> #1 0x00000000006bfa49 in MolFilePlugin::read_metadata(Molecule*) ()
> #2 0x0000000000740bf9 in VMDApp::molecule_load(int, char const*, char
> const*, FileSpec const*) ()
> #3 0x00000000007b8ecb in FileChooserFltkMenu::load_cb(Fl_Widget*, void*)
> ()
> #4 0x0000000000b36c16 in Fl_Button::handle(int) ()
> #5 0x0000000000b31f2e in ?? ()
> #6 0x0000000000b32211 in Fl::handle(int, Fl_Window*) ()
> #7 0x0000000000b48d1d in fl_handle(_XEvent const&) ()
> #8 0x0000000000b498fb in ?? ()
> #9 0x0000000000b49d2f in fl_wait(double) ()
> #10 0x0000000000b317bd in Fl::wait(double) ()
> #11 0x000000000077322a in VMDupdateFltk() ()
> #12 0x0000000000775420 in main ()
> (gdb)
> I am using latest vmd release: "VMD 1.9.2 OpenGL" on UBUNTU 14.04 64-bit
> I would appreciate any guidances
> Best Regards,
> Nima Soltani
> ----------------------------------------------------------
> Graduate Student of Physical Chemistry
> Department of Chemistry,
> Sharif University of Technology.
> =================================
> ---------- Forwarded message ----------
> From: Nima Soltani <[1]nima.slt_at_gmail.com>
> Date: Fri, Mar 13, 2015 at 12:13 AM
> Subject: Segmentation fault (core dump)
> To: [2]vmd-l_at_ks.uiuc.edu
>
> References
>
> Visible links
> 1. mailto:nima.slt_at_gmail.com
> 2. mailto:vmd-l_at_ks.uiuc.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/