[gmx-users] Fwd: Problem in applying walls in the z direction

[Justin Lemkul]

On 7/2/16 3:50 PM, Stephen Chan wrote:
> Dear all,
>
> I'm running a simulation of a bilayer system and I would like to apply wall
> condition to both xy planes (i.e. nwall = 2). On top of the normal MD settings,
> I added a couple of lines to the mdp file:
> pbc             = xy
> nwall           = 2
> wall-type       = 10-4
> wall-density    = 5  5
> wall-atomtype   = OT OT
> ewald-geometry  = 3dc
>
> integrator              = md
> dt                      = 0.002
> nsteps                  = 50000000
> nstlog                  = 10000
> nstxout                 = 0
> nstvout                 = 0
> nstfout                 = 0
> nstcalcenergy           = 10000
> nstenergy               = 10000
> nstxout-compressed      = 10000
> ;
> cutoff-scheme           = Verlet
> nstlist                 = 20
> rlist                   = 1.0
> coulombtype             = pme
> rcoulomb                = 1.0
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 0.9
> rvdw                    = 1.0
> ;
> tcoupl                  = Nose-Hoover
> tc_grps                 = PROT   MEMB   SOL_ION
> tau_t                   = 1.0    1.0    1.0
> ref_t                   = 310 310 310
> ;
> pcoupl                  = Parrinello-Rahman
> pcoupltype              = semiisotropic
> tau_p                   = 5.0
> compressibility         = 0.0     4.5e-5
> ref_p                   = 1.0     1.0
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> continuation            = yes
> ;
> nstcomm                 = 100
> comm_mode               = linear
> comm_grps               = PROT   MEMB   SOL_ION
> ;
> refcoord_scaling        = com
>
> When running grompp, I managed to generate the tpr file from my input
> gro file. However, when running mdrun, I got the following error:
>
> Fatal error:
> There is no domain decomposition for 84 ranks that is compatible with
> the given box and a minimum cell size of 14.9422 nm
> Change the number of ranks or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
>
> Any help would be appreciated :)
>

The error message tells you where to start:

"Look in the log file for details on the domain decomposition"

What do you find there?  You have bonded interactions at very long distances, 
and the .log file tells you exactly which atoms are engaged in the limiting 
interactions.

-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

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