[gmx-users] Segmentation fault in g_traj with -mol opion

[Steve Fiedler]

Gromacs users,

Upon application of the g_traj (4.0.x) utility with the -mol option in 
the extraction of coordinates, velocities and forces, I have encountered 
a segmentation fault.  This problem does not occur using the g_traj 
utility from version 3.3.1.  To demonstrate, below I have included input 
files for a two atom system.  After the completion of a calculation, 
g_traj is invoked (for example) with the run parameters:  g_traj -n 
index.ndx -noxvgr -ox output.dat -mol

Using the trajectory obtained from the demonstration input, the output 
for version 3.3.1 exits normally, and g_traj from 4.0.2 and 4.0.99 
terminates with:

Group     0 (      System) has     2 elements
Group     1 (         HEL) has     2 elements
Select a group: 1
Selected 1: 'HEL'
./m++: line 1: 14058 Segmentation fault      g_traj -n index.ndx -noxvgr 
-ox ouputfilename -mol

Assistance with this problem would be appreciated.
Thank you,

Steve Fiedler


conf.gro
--------
Helium
    2
    1HEL     He    1   1.000   1.000   1.000
    2HEL     He    2   2.000   2.000   2.000
   5.00000   5.00000   5.00000
------------------------------------------------------------

grompp.mdp
----------
integrator               = md
dt                       = 0.001
nsteps                   = 1000
ns_type                  = grid
pbc                      = xyz
coulombtype              = shift
rlist                    = 0.9
rcoulomb                 = 0.9
rvdw                     = 0.9
tcoupl                   = no
pcoupl                   = no
gen-vel                  = yes
gen-temp                 = 300

nstxout                  = 1
nstvout                  = 1
nstfout                  = 1
------------------------------------------------------------

topol.top
-------
[ defaults ]
1     3     yes      0.125  0.5

[ atomtypes ]
   He     4.0000    0.000  A     0.2600      0.080000

[ moleculetype ]
 HEL             1

[ atoms ]
     1    He      1  HEL      He      1     0.00000     4.00000

[ system ]
Helium

[ molecules ]
 HEL        2
------------------------------------------------------------

index.ndx
-------
[ System ]
   1    2
[ HEL ]
   1    2