[gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

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
>