On 19/11/2011 10:10 PM, Igor Druz wrote:
Hello,
I am running MDs on a linux PC with OpenSuse, using:
mpirun -np 4 mdrun -v -dlb auto -reprod ....
If I repeat the calculation on the same PC, I get the same result. If
I change to another PC with RedHat I get a different result.
Yep. http://www.gromacs.org/Documentation/Terminology/Reproducibility
More specifically, I am calculating a deviation from experiment, which
varies by ~20 % on changing operating systems (pretty much the same
hardware on both PCs). Is there any way to avoid such variations? I
guess I am missing something in the mdp file, which is:
Change your gen_vel seed and I bet you observe a similar variation on
the same machine. There are rather few systems that will have
equilibrated in 2ns, never mind converged.
Mark
cpp = /usr/bin/cpp -traditional
integrator = sd
tinit = 0
dt = 0.002
nsteps = 1000000
nstcomm = 1
nstcalcenergy = 1
nstxout = 5
nstvout = 100
nstlog = 100
nstenergy = 100
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 0.9
optimize_fft = yes
coulombtype = pme
rcoulomb = 0.9
epsilon-r = 1
rvdw = 0.9
constraints = all-bonds
constraint-algorithm = Lincs
unconstrained-start = yes
lincs-warnangle = 30
tc_grps = System
tau_t = 0.1
ref_t = 300.0
Pcoupl = parrinello-rahman
tau_p = 2
compressibility = 4.5e-05
ref_p = 1.0
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Many thanks for your help,
Igor
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