[gmx-users] "No atom pairs for dispersion correction" Warning from GROMACS 2020 mdrun

[Eric Legresley]

Hello All,

I am performing a gpu accelerated simulation on a 292683 atom system (a solvated multimeric protein) using the amber99sb-ildn forcefield.

Grompp does not throw any errors or warnings.  However, mdrun throws the following warning prior to simulation:

WARNING: There are no atom pairs for dispersion correction

The machine has an i7-8750H CPU with a GTX 1050Ti GPU, and is running GROMACS 2019.3.

However, when I run the exact same system on another machine with a Ryzen 5 3600 CPU with a GTX 1650 Super GPU running GROMACS 2020, I do not get this warning.

What could be causing this warning?  Is it due to the difference in GROMACS versions?  Has anything changed between versions that would cause a warning like this?

Thanks,
Eric

My production .mdp is as follows:

integrator   = md            ; leap-frog integrator
nsteps       = 5000000       ; 2 * 5,000,000 = 10 ns
dt           = 0.002         ; 2 fs
comm-mode    = Linear        ; remove center of mass translation


nstxout                = 25000      ; save coordinates to .trr every 50ps
nstvout                = 25000      ; save velocities to .trr every 50ps
nstfout                = 0          ; don't save forces to .trr
nstxout-compressed     = 25000      ; xtc compressed trajectory output every 50ps
compressed-x-precision = 1000       ; precision with which to write to the compressed trajectory file
nstlog                 = 25000      ; log every 50 ps
nstenergy              = 2500       ; save energies every 5 ps
nstcalcenergy          = 100        ; calculate energies every 100 steps


constraint_algorithm   = lincs      ; holonomic constraints
constraints            = h-bonds    ; h bonds are constrained
continuation           = yes        ; not first run


cutoff-scheme   = Verlet
ns-type         = grid   ; search neighboring grid cells
nstlist         = 20     ; irrelevent with Verlet
pbc             = xyz    ; 3D PBC


coulombtype      = PME      ; Particle Mesh Ewald for long-range electrostatics
rcoulomb         = 1.0      ; short-range electrostatic cutoff (in nm)
ewald_geometry   = 3d       ; Ewald sum is performed in all three dimensions
pme-order        = 4        ; interpolation order for PME (default is 4)
fourierspacing   = 0.12     ; grid spacing for FFT (default is 0.12)
ewald-rtol       = 1e-6     ; relative strength of the Ewald-shifted direct potential at rcoulomb


vdw-type                = Cut-off
vdw-modifier            = Potential-shift-Verlet
verlet-buffer-tolerance = 0.005        ; replaces/defines rlist (default 0.005)
rvdw                    = 1.0          ; short-range van der Waals cutoff (in nm)
DispCorr                = EnerPres     ; apply long range dispersion corrections for Energy and Pressure


tcoupl           = nose-hoover
tc_grps          = protein non-protein
tau_t            = 1.0 1.0
ref_t            = 310 310

pcoupl           = parrinello-rahman
pcoupltype       = isotropic
tau_p            = 5.0                  ; time constant (ps)
ref_p            = 1.0                  ; reference pressure (bar)
compressibility  = 4.5e-05              ; isothermal compressibility of water (bar^-1)
refcoord-scaling = all


gen_vel      = no      ; Velocity generation is off