Daniel Adriano Silva M wrote:
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.
Yes, it's known. IIRC there was some discussion on the developers list
about changing the relevant data type so that it can store bigger
numbers. It's also a non-problem inasmuch as if you are ever able to run
a simulation that long, manually resetting the number of steps to zero
at a suitable point will be workable.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
