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Here post your question : Energy minimisation gives following error for biphasic system(cyclohexane-water)-
Program: gmx mdrun, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/domdec/domdec.cpp (line 2263)
MPI rank: 0 (out of 20)
Fatal error:
There is no domain decomposition for 16 ranks that is compatible with the
given box and a minimum cell size of 4.86065 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
I have attached my em.log file for reference. em.log (14.4 KB)
Kindly help me to resolve this.
my minim.mdp file-
; 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
Is my system energy minimized or is there some mistake here. I think it’s too high.
