Error in the EM run

User discussions
1

Hey,
I am starting out with GROMACS!
I need to perform an Energy Minimization. For the EM run while using the mdrun I am getting this error message:

Fatal error:
There is no domain decomposition for 32 ranks that is compatible with the
given box and a minimum cell size of 8.76596 nm
Change the number of ranks or mdrun option -rdd or -dds

If anyone can please help me in this regard that will be great!

p.s. The parameter file I’m using can be found below:
; LINES STARTING WITH ‘;’ ARE COMMENTS
title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; long range electrostatic cut-off
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
DispCorr = no

2

Hi, if your minimum DD cell size is almost 9 nm, that usually means a really long bond or something otherwise strange in your system setup.

There simple way around this would be to run gmx mdrun on 1 or 2 CPUs, but the original problem might persist even if the minimization completes, so first use it to diagnose the issue that caused the error in the first place (e.g. by comparing the structures before and after minimization).

1 Like
4

Thank you…