VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 25 2015 - 15:04:34 CDT

Hi,
  This sounds like the bug that was fixed in the updated version of
the Gromacs plugins (which also contain .gro support):
  http://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Sep 24, 2015 at 08:15:28PM -0600, Eric Smoll wrote:
> Hello VMD users,
>
> I am trying to load and process a GROMACS file on a new remote computer
> where I have installed VMD 1.9.2. For some reason, attempting to load a
> ".gro" file interactively works but the same command in a script causes a
> segmentation fault. This occurs with and without the "--dispdev none" flag.
>
> [ script61_sas ] $ *vmd -e script61.tcl -args script61_c_2000.gro
> atomarea_2000.ndx script61_o_2000.txt out_2000.txt*
> Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> 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, 32 CPUs detected.
> Info) Free system memory: 55969MB (86%)
> Info) Dynamically loaded 2 plugins in directory:
> Info)
> /mnt/lustrefs/store/group/kaptonlab/vmd-build/1.9.2/lib/plugins/LINUXAMD64/molfile
> *Segmentation fault*
>
> [ script61_sas ] $ *vmd*
> Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> 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, 32 CPUs detected.
> Info) Free system memory: 55970MB (86%)
> Info) Dynamically loaded 2 plugins in directory:
> Info)
> /mnt/lustrefs/store/group/kaptonlab/vmd-build/1.9.2/lib/plugins/LINUXAMD64/molfile
> vmd > *mol new script61_c_2000.gro*
> Info) Using plugin gro for structure file script61_c_2000.gro
> Info) Using plugin gro for coordinates from file script61_c_2000.gro
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 35802
> Info) Bonds: 34749
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 2106
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 2106 Protein: 0 Nucleic: 0
> 0
> Info) Finished with coordinate file script61_c_2000.gro.
> vmd >
>
> I am certain this is the command causing the failure (a "puts" command
> after the "mol new script61_c_2000.gro" line is not executed. My compiling
> options are:
> LINUXAMD64 IMD NETCDF TCL PTHREADS SILENT
>
> Best,
> Eric 

-- 
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/