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
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