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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