[gmx-users] grompp vel_gen = seg fault
roland at utk.edu
Sun Mar 22 23:55:07 CET 2009
do you get any other error messages? (Check md.log and the output)
You might want to use 4.0.4 instead of 4.0.2. (Some bugs have been fixed)
2009/3/22 KS Rotondi <ksr at chemistry.umass.edu>:
> Dearest All,
> I'm experiencing strange behavior running Gromacs 4.0.2 on dual G5
> macintoshs (OS 10.4.11) in my college's computer laboratory. When I use the
> attached .mdp file, grompp ends in a seg fault, however if I remove the last
> 3 lines (controlling velocity generation) grompp runs normally and generates
> a working .tpr file. In fact, simply changing gen_vel to no removes the
> segmentation fault. To further complicate matters, this behavior is not seen
> on my personal dual G5 running 10.5.4 (i.e. the attached .mdp file works
> without modifications).
> Does anyone have any insight into this behavior?
> Thanks in advance,
> include = -I../top
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 15000 ; total 30 ps.
> nstxout = 5000 ; cord to .trr file every 10 ps.
> nstvout = 5000 ; velo to .trr file every 10 ps.
> nstfout = 5000 ; force to .trr file every 10 ps.
> nstlog = 5000 ; energ to log file every 10ps.
> nstenergy = 250 ; energ to energ file every 0.5ps
> nstxtcout = 250 ; cood to .xtc file every 0.5ps
> xtc_grps = Protein SOL
> nstlist = 5 ; freq (steps) update neighbor list
> ns_type = grid
> pbc = xyz ; turns on periodic bound. cond.
> rlist = 1.5
> coulombtype = PME
> rcoulomb = 1.5
> vdwtype = switch
> rvdw = 1.4
> rvdw_switch = 1.0
> ; Berendsen temperature coupling is on in two groups
> tcoupl = Berendsen
> tc_grps = Protein SOL
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Energy monitoring
> energygrps = Protein SOL
> ; Generate velocities is on at 300 K.
> gen_vel = yes
> gen_temp = 300
> gen_seed = -1
> Dr. K.S. Rotondi
> Departments of Chemistry, BIochemistry and Molecular Biology
> 914G LGRT
> The University of Massachusetts - Amherst
> Amherst, MA 01003
> "If there's a solution, why worry?, If there's no solution, why worry?"
> His Holiness, the Dalai Llama
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