Hi Justin,
Just above the fatal error message, there is some additional information:
Initializing Domain Decomposition on 112 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 10.867 nm, Exclusion, atoms 30544 30545
multi-body bonded interactions: 0.488 nm, CMAP Dih., atoms 1075 1091
Minimum cell size due to bonded interactions: 11.954 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm
Estimated maximum distance required for P-LINCS: 0.222 nm
Guess for relative PME load: 0.23
Will use 84 particle-particle and 28 PME only ranks
This is a guess, check the performance at the end of the log file
Using 28 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 84 cells with a minimum initial size of 14.942 nm
The maximum allowed number of cells is: X 0 Y 0 Z 2
Do I need to adjust other parameters in the mdp accordingly??
Stephen
On 07/02/16 22:02, Justin Lemkul wrote:
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
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
