[gmx-users] grompp vel_gen = seg fault

[Roland Schulz]

Hi,

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)

Roland

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,
>
> Ken
>
> 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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