Dear GROMACS users and developers.
I don known if this issued had been previously addressed, but I found
that when I try to run a MD with time-step of 2fs and 2500000000 steps
(yes 500us!!!) the dynamics aborts with the next message (64bit-LINUX
and icc 10 compiler):
####################
WARNING: This run will generate roughly 20576946697451257856 Mb of data
starting mdrun 'F1-ATPASE'
-1794967296 steps, -3589934.8 ps.
nodetime = 0! Infinite Giga flopses!
Parallel run - timing based on wallclock.
#####################
If i reduce the steps number by one order of magnitude then all goes
ok. My MDP when I obtined this error was:
; VARIOUS PREPROCESSING OPTIONS
title = NPT simulacion
cpp = /lib/cpp
; RUN CONTROL PARAMETERS
integrator = md
dt = 0.002
nsteps = 2500000000
nstxout = 5000
nstvout = 5000
nstlog = 2500
nstenergy = 2500
nstxtcout = 2500
energygrps = Protein Non-Protein
nstlist = 10
rlist = 1.0
ns_type = grid
pbc = xyz
coulombtype = pme
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
fourierspacing = 0.12
pme_order = 4
optimize_fft = yes
ewald_rtol = 1e-5
tcoupl = Berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
Pcoupl = Parrinello-Rahman
Pcoupltype = Isotropic
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
gen_vel = no
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = yes
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
I known this kind of error is not a priority since the total
integration time is ridiculous big, but anyway I want to comment it to
you.
Thanks
Daniel Silva
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