[gmx-users] Error in BlueGene
Cintia C. Vequi-Suplicy
cintia at if.usp.br
Wed Jan 30 18:44:53 CET 2013
Mark,
Thank you for your answer.
I did an energy minimization with the file em.mdp (below) and then I did
a 40 ns simulation with the same md.mdp I send before. These two steps
were done in my local cluster.
After that I took the configuration for the simulation in the bluegene
and I got these error. I notice that the step that the error occurs
depends on the number of nodes I use.
I am also including the end of the min.out file.
I also tried others integrators for the energy minimization but I always
get the same error.
Thank you again,
Cíntia
-------------------------------------------------------
em.mdp
integrator = steep
tinit = 0.0
dt = 0.002
nsteps = 5000000
nstcomm = 1
comm-grps = Other SOL
nstxout = 100
nstvout = 100
nstfout = 0
nstlog = 100
nstenergy = 100
nstxtcout = 100
xtc_precision = 100
xtc-grps =
energygrps = Other SOL
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = reaction-field
rcoulomb = 1.4
epsilon_rf = 66
vdw_type = cut-off
rvdw = 1.4
DispCorr = No
constraints = none
-------------------------------------------------------
min.out
...
Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
atom= 22015
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 5199 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.79302464181879e+06
Maximum force = 6.65022934447791e+02 on atom 22015
Norm of force = 4.90065871184878e+00
gcq#0: Thanx for Using GROMACS - Have a Nice Day
-------------------------------------------------------
>
>
> -------------------------------------------------------
> md.mdp file
>
>
> integrator = md
> tinit = 0.0
> dt = 0.002
> nsteps = 5000000
> nstcomm = 5
> comm-grps = Other SOL
>
> nstxout = 1000
> nstvout = 1000
> nstfout = 0
> nstlog = 1000
> nstenergy = 1000
> nstxtcout = 1000
> xtc_precision = 1000
> xtc-grps =
> energygrps = Other SOL
>
> nstlist = 5
> ns_type = grid
> pbc = xyz
> rlist = 1.4
>
> coulombtype = reaction-field
> rcoulomb = 1.4
> epsilon_rf = 66
>
> vdw_type = cut-off
> rvdw = 1.4
> DispCorr = No
>
> tcoupl = v-rescale
> tc-grps = Other SOL
> tau_t = 0.4 0.4
> ref_t = 296 296
>
> Pcoupl = berendsen
> Pcoupltype = semiisotropic
> tau_p = 0.2 0.2
> compressibility = 4.51e-5 4.51e-5
> ref_p = 1.0 1.0
>
> constraints = hbonds
> constraint_algorithm = lincs
>
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