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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
