[gmx-users] mdrun

[Mark Abraham]

On 28/03/2011 7:06 PM, michael zhenin wrote:
> Dear all,
> I am trying to run dynamics (mdrun) on GROMACS 4.5.3 in parallel on 8 
> processors, but it crashes after a while and refuses to reach to the end.
> The error note that pops out is:
>
> 1 particles communicated to PME node 4 are more than 2/3 times the cut-off
>
> >> out of the domain decomposition cell of their charge group in 
> dimension y.
>
> >> This usually means that your system is not well equilibrated

So either your system is not well equilibrated, or your topologies don't 
match reality. See 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark

> My system contains protein, ATP and Mg. I have equilibirated it for 
> 300 ps that were divided into 3 parts.
> The first 2 parts were the NVT equilibiration (the first one was made 
> in order to equilibrate only the water) - 100 ps each.
>
>
> The third was the NPT - 100 ps.
> The system wasn't constraint.
>
> My mdp file is :
>
> title = OPLS wt nbd1 MD
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 20000000 ; 1 * 20000000 = 20000 ps, 20 ns
>
>
> dt = 0.001 ; 1 fs
> ; Output control
> nstxout = 20000 ; save coordinates every 2 ps
> nstvout = 20000 ; save velocities every 2 ps
> nstxtcout = 20000 ; xtc compressed trajectory output every 2 ps
> nstenergy = 20000 ; save energies every 2 ps
>
>
> nstlog = 20000 ; update log file every 2 ps
> ; Bond parameters
> continuation = yes ; Restarting after NPT
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cels
> nstlist = 5 ; 10 fs
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
>
>
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> ewald_rtol = 1e-05
>
>
> fourierspacing = 0.12 ; grid spacing for FFT
> pme_order = 6 ;
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein Non-Protein ; two coupling groups - more accurate
>
>
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 300 300 ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype = isotropic ; uniform scaling of box vectors
>
>
> tau_p = 1.0 ; time constant, in ps
> ref_p = 1.0 ; reference pressure, in bar
> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
>
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no ; Velocity generation is off
> morse = yes
>
>
> I've searched the net for this error and didn't find any answer. Did 
> anybody see this error? and what should i do with it..
>
> Thanks,
>
> Michael
>

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