GROMACS version: 2021.4
GROMACS modification: Yes/No
Here post your question : I am simulating a protein-cyclohexane system. The protein is ~8.2 kDa. I am using charmm36 forcefield. The system is to be simulated at 290K and 310K. But at both temperatures, after NVT equilibration, I am getting the following notes-
NOTE: PME load balancing increased the non-bonded workload by more than 50%.
For better performance, use (more) PME ranks (mdrun -npme),
or if you are beyond the scaling limit, use fewer total ranks (or nodes).
Dynamic load balancing report:
DLB got disabled because it was unsuitable to use.
Average load imbalance: 33.0%.
The balanceable part of the MD step is 47%, load imbalance is computed from this.
Part of the total run time spent waiting due to load imbalance: 15.5%.
Average PME mesh/force load: 1.314
Part of the total run time spent waiting due to PP/PME imbalance: 11.8 %
NOTE: 15.5 % of the available CPU time was lost due to load imbalance
in the domain decomposition.
You can consider manually changing the decomposition (option -dd);
e.g. by using fewer domains along the box dimension in which there is
considerable inhomogeneity in the simulated system.
NOTE: 11.8 % performance was lost because the PME ranks
had more work to do than the PP ranks.
You might want to increase the number of PME ranks
or increase the cut-off and the grid spacing.
The nvt.mdp file-
title = charmm36 Protein-CYHE system NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1000 ps
dt = 0.002 ; 2 fs
; Output control
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
nstxout-compressed = 500 ; save coordinates every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds to H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 20 ; largely irrelevant with Verlet
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 1.0 1.0 ; time constant, in ps
ref_t = 290 290 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction is not used for proteins with the C36 additive FF
DispCorr = no
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 290 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
Can the notes be ignored and proceed to NPT equilibration?