Hello Gromacs Community, I am trying to calculate the solvation free energy of a hBN sheet following Justin Lemkul and Alchemistry's tutorials. Since the hBN sheet is infinitely large, I turned the periodic molecules flag on. This runs all fine on one core, but when I try to run NVT in parallel (e.g. 4 ranks), the job would throw the following error:
A list of missing interactions: LJC Pairs NB of 890400 missing 338688 ------------------------------------------------------- Program gmx mdrun, VERSION 5.1.4 Source code file: /gpfs/runtime/opt/gromacs/5.1.4/src/gromacs-5.1.4/src/gromacs/domdec/domdec_topology.cpp, line: 242 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Halting parallel program gmx mdrun on rank 1 out of 4 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1) ------------------------------------------------------- Program gmx mdrun, VERSION 5.1.4 Source code file: /gpfs/runtime/opt/gromacs/5.1.4/src/gromacs-5.1.4/src/gromacs/domdec/domdec_topology.cpp, line: 242 Software inconsistency error: Some interactions seem to be assigned multiple times For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- It seems like a domain decomposition error. My first thought was that the system "explode". However, when I check my topology and pbc condition carefully, there is no sign of anything wrong. I also tried NPT & PROD MD. The same error when I ran on multiple MPI threads. My question is: why the system could run fine on one MPI, but not if I increased the number of MPI threads? Any help on this issue will be really appreciated. Here below is my .mdp file: ; RUN CONTROL—NVT ;—————————————————————————— define = -DPOSRES_HBN integrator = sd ; stochastic leap-frog integrator nsteps = 5000 ; 2 * 5,000 fs = 10 ps dt = 0.002 ; 2 fs comm-mode = Linear ; remove center of mass translation nstcomm = 100 ; frequency for center of mass motion removal ;—————————————————————————— ; OUTPUT CONTROL ;—————————————————————————— nstxout = 0 ; don't save coordinates to .trr nstvout = 0 ; don't save velocities to .trr nstfout = 0 ; don't save forces to .trr nstxout-compressed = 5000 ; xtc compressed trajectory output every 5000 steps compressed-x-precision = 1000 ; precision with which to write to the compressed trajectory file nstlog = 5000 ; update log file every 10 ps nstenergy = 5000 ; save energies every 10 ps nstcalcenergy = 100 ; calculate energies every 100 steps ;—————————————————————————— ; BONDS ;—————————————————————————— constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; hydrogens only are constrained lincs_iter = 1 ; accuracy of LINCS (1 is default) lincs_order = 4 ; also related to accuracy (4 is default) lincs-warnangle = 30 ; maximum angle that a bond can rotate before LINCS will complain (30 is default) continuation = no ; formerly known as 'unconstrained-start' - useful for exact continuations and reruns ;—————————————————————————— ; NEIGHBOR SEARCHING ;—————————————————————————— cutoff-scheme = Verlet ns-type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs (default is 10) rlist = 1.2 ; short-range neighborlist cutoff (in nm) pbc = xyz ; 3D PBC ; PBC: grp is infinite periodic-molecules = yes ;—————————————————————————— ; ELECTROSTATICS ;—————————————————————————— coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.2 ; 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 = 0.16 ; grid spacing for FFT ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb ;—————————————————————————— ; VDW ;—————————————————————————— vdw-type = PME rvdw = 1.2 vdw-modifier = Potential-Shift ewald-rtol-lj = 1e-3 lj-pme-comb-rule = Geometric DispCorr = EnerPres ;—————————————————————————— ; TEMPERATURE & PRESSURE COUPL ;—————————————————————————— tc_grps = System tau_t = 0.1 ref_t = 300 pcoupl = no ;—————————————————————————— ; VELOCITY GENERATION ;—————————————————————————— gen_vel = yes ; Velocity generation is on (if gen_vel is 'yes', continuation should be 'no') gen_seed = -1 ; Use random seed gen_temp = 300 ;—————————————————————————— ; FREE ENERGY CALCULATIONS ;—————————————————————————— free-energy = yes couple-moltype = BNT couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no separate-dhdl-file = yes sc-alpha = 0.5 sc-power = 1 sc-sigma = 0.3 init-lambda-state = 0 coul-lambdas = 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 nstdhdl = 100 calc-lambda-neighbors = -1 Best, Xuliang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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