[gmx-users] error in mdrun

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Mon Jul 9 15:25:31 CEST 2012

Hi everybody,
I want to do a md for a protein with a membrane around it.
I already minimised the energy of the protein.

Output of the minimization:

^MStep=  812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02,
atom= 1653
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10

Double precision normally gives you higher accuracy.
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 813 steps,
but did not reach the requested Fmax < 10.
Potential Energy  = -7.5928356e+05
Maximum force     =  3.6197971e+02 on atom 1653
Norm of force     =  2.6517429e+00

In my eyes this output was okey so I went on with the md.
And here I get the error:

Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated

I already read the error page for this error and also the blowing up page
but I still do not know what to do now.

My .mdp file for the md runs looks like this:

define          = -DPOSRES
integrator              = md
dt                      = 0.005
nsteps          = 2000
nstxout         = 0
nstvout         = 0
nstfout         = 0
nstlog          = 1000
nstxtcout               = 0
nstenergy               = 5
energygrps              = Protein Non-Protein
nstcalcenergy   = 5
nstlist         = 10
ns-type         = Grid
pbc                     = xyz
rlist           = 0.9
coulombtype             = PME
rcoulomb                = 0.9
rvdw            = 0.9
fourierspacing          = 0.12
pme_order               = 4
ewald_rtol              = 1e-5
gen_vel         = yes
gen_temp                = 200.0
gen_seed                = 9999
constraints             = all-bonds

Are here any optinos which can cause the error?


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