[gmx-users] nvt error

[Justin Lemkul]

On 11/2/15 9:13 AM, Urszula Uciechowska wrote:
>
>
> Hi,
>
> During nvt simulations I obtained an error message:
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 5.0.6
> Source code file:
> /scratch/60488192.batch.grid.cyf-kr.edu.pl/gromacs-5.0.6/src/gromacs/mdlib/pme.c,
> line: 754
>
> Fatal error:
> 11 particles communicated to PME rank 3 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge
>   group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Error on rank 15, will try to stop all ranks
> Halting parallel program mdrun_mpi on CPU 15 out of 32
>
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 5.0.6
> Source code file:
> /scratch/60488192.batch.grid.cyf-kr.edu.pl/gromacs-5.0.6/src/gromacs/mdlib/pme.c,
> line: 754
>
> Fatal error:
> 1 particles communicated to PME rank 4 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge
> group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Error on rank 19, will try to stop all ranks
> Halting parallel program mdrun_mpi on CPU 19 out of 32
>
>
>
> My nvt input file is:
>
> ; 7.3.2 Preprocessing
> define                  = -DPOSRES
>
> ; 7.3.3 Run Control
> integrator              = md
> tinit                   = 0
> dt                      = 0.002
> nsteps                  = 100000
> comm_mode               = Linear
> nstcalcenergy           = 1
> comm_grps               = Protein Non-Protein
>
> ; 7.3.8 Output Control
> nstxout                 = 25000
> nstvout                 = 25000
> nstfout                 = 25000
> nstlog                  = 100
> nstenergy               = 100
> nstxtcout               = 100
> xtc_precision           = 1000
> xtc_grps                = System
> energygrps              = System
> cutoff-scheme           = verlet
> ; 7.3.9 Neighbor Searching
> nstlist                 = 10
> ns_type                 = grid
> pbc                     = xyz
> rlist                   = 0.9
>
> ; 7.3.10 Electrostatics
> coulombtype             = PME
> rcoulomb                = 0.9
>
> ; 7.3.11 VdW
> vdwtype                 = cut-off
> rvdw                    = 0.9
> DispCorr                = EnerPres
>
> ; 7.3.13 Ewald
> fourierspacing          = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
>
> ; 7.3.14 Temperature Coupling
> tcoupl                  = V-rescale
> tc_grps                 = Protein    Non-Protein
> tau_t                   = 0.1        0.1
> ref_t                   = 300        300
>
> ; 7.3.17 Velocity Generation
> gen_vel                 = yes
> gen_temp                = 310
> gen_seed                = -1
>
> ; 7.3.18 Bonds
> constraints             = all-bonds
> constraint_algorithm    = LINCS
> continuation            = no
> lincs_order             = 4
> lincs_iter              = 1
> lincs_warnangle         = 30
>
> What is wrong in the input file?
>

There is no reason for separate comm-grps for a simple protein system. 
Otherwise, 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System 
and the million or so other threads in the archive about dealing with instability.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================