VMD-L Mailing List

From: Eric Smoll (ericsmoll_at_gmail.com)
Date: Thu Sep 24 2015 - 21:15:28 CDT

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