[gmx-users] Error in BlueGene

[Ricardo Soares]

Hello,

before submitting to Bluegene, I always test the system in my local 8 core
cpu, and if it works, it will also work in Bluegene, as long as I balance the
domain decomposition for the larger number of cores. If your system insists in
exploding, even after energy minimization, you could try to decrease the
integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in
some cases even 0.5 fs. Did you tried that?

Cheers,

Ricardo.



On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote
> 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
> >
> 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 
> * Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org. * Can't post? 
> Read http://www.gromacs.org/Support/Mailing_Lists