[gmx-users] domain decomposition error in the energy minimization step

[Qasim Pars]

Dear users,

I am trying to simulate a protein-ligand system including ~20000 atoms with
waters using GROMACS-2016.1. The protocol I tried is forward state for the
free energy calculation. The best ligand pose used in the simulations was
got by AutoDock. At the beginning of the simulation GROMACS suffers from
domain decomposition error in the energy minimization step:

Fatal error:
There is no domain decomposition for 20 ranks that is compatible with the
given box and a minimum cell size of 1.7353 nm
Change the number of ranks or mdrun option -rdd
Look in the log file for details on the domain decomposition

I checked the complex structure visually. I don't see any distortion in the
structure. To check whether the problem is the number of nodes, I used 16
nodes:

gmx mdrun -v -deffnm em -nt 16

The energy minimization step was completed successfully. For the NVT step I
used 16 nodes again.

gmx mdrun -v -deffnm nvt -nt 16

After ~2000000 steps the system gave too many lincs warning.

Whereas there is no problem with wild type protein when it is simulated
without using -nt 16. These domain decomposition error and lincs warning
arise for complex structure.

By the way to keep the ligand in the active site of protein I use the bond,
angle and dihedral restraints under [ intermolecular_interactions ] section
in the top file.

[ intermolecular_interactions ]
[ bonds ]
  313    17 10     0.294     0.294    10.000      0.000     0.294
0.294    10.000   4184.000

[ angle_restraints ]
  312   313    17   313          1   140.445      0.000          1
140.445     41.840          1
  313    17    19    17          1   107.175      0.000          1
107.175     41.840          1

[ dihedral_restraints ]
  300   312   313    17          1    56.245     0.000      0.000
56.245     0.000     41.840
  312   313    17    19          1    -3.417     0.000      0.000
-3.417     0.000     41.840
  313    17    19    14          1  -110.822     0.000      0.000
-110.822     0.000     41.840

The mdp file used for the energy minimization is follows:

define              = -DFLEXIBLE
integrator          = steep
nsteps              = 50000
emtol               = 1000.0
emstep              = 0.01
nstcomm             = 100

; OUTPUT CONTROL
nstxout-compressed        = 500
compressed-x-precision    = 1000
nstlog                    = 500
nstenergy                 = 500
nstcalcenergy             = 100

; BONDS
constraints         = none

; NEIGHBOUR SEARCHING

cutoff-scheme    = verlet
ns-type          = grid
nstlist          = 10
pbc              = xyz

; ELECTROSTATICS & EWALD
coulombtype      = PME
rcoulomb         = 1.0
ewald_geometry   = 3d
pme-order        = 4
fourierspacing   = 0.12

; VAN DER WAALS
vdwtype         = Cut-off
vdw_modifier    = Potential-switch
rvdw            = 1.0
rvdw-switch     = 0.9
DispCorr        = EnerPres

; FREE ENERGY
free-energy              = yes
init-lambda              = 0
delta-lambda             = 0
sc-alpha                 = 0.3
sc-power                 = 1
sc-sigma                 = 0.25
sc-coul                  = yes
couple-moltype           = ligand
couple-intramol          = no
couple-lambda0           = vdw-q
couple-lambda1           = none
nstdhdl                  = 100

I removed the free energy lines in the em.mdp and [
intermolecular_interactions ] section in the top file but GROMACS still
gives the domain decomposition error for the complex structure.

Will you please give suggestions on getting rid of the lincs warning and
domain decomposition messages?

I would appreciate any kind of help.

Thanks.

-- 
Qasim Pars