[gmx-users] Fatal error during mdrun
Samayaditya Singh
ssamayaditya at yahoo.com
Tue Nov 19 14:52:21 CET 2019
Hi ,I am having an error during running the mdrun for homo-dimer of a protein-ligand complex of Ribokinase on server, I used Charmm36 FF parameters for both ligands and protein. can u please give some advice.
Changing nstlist from 10 to 20, rlist from 1 to 1.028
Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 10000000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 1535035550 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstcalcenergy = 100 nstenergy = 5000 nstxout-compressed = 5000 compressed-x-precision = 5000 cutoff-scheme = Verlet nstlist = 20 ns-type = Grid pbc = xyz periodic-molecules = FALSE verlet-buffer-tolerance = 0.005 rlist = 1.028 rlistlong = 1.028 nstcalclr = 10 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-shift rvdw-switch = 0 rvdw = 1 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.16 fourier-nx = 72 fourier-ny = 72 fourier-nz = 72 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 implicit-solvent = No gb-algorithm = Still nstgbradii = 1 rgbradii = 1 gb-epsilon-solvent = 80 gb-saltconc = 0 gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = 2.05016 tcoupl = V-rescale nsttcouple = 10 nh-chain-length = 0 print-nose-hoover-chain-variables = FALSE pcoupl = Parrinello-Rahman pcoupltype = Isotropic nstpcouple = 10 tau-p = 2 compressibility (3x3): compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} ref-p (3x3): ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = FALSE QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = TRUE Shake-SOR = FALSE shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = FALSE rotation = FALSE interactiveMD = FALSE disre = No disre-weighting = Conservative disre-mixed = FALSE dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = FALSE E-x: n = 0 E-xt: n = 0 E-y: n = 0 E-yt: n = 0 E-z: n = 0 E-zt: n = 0 swapcoords = no adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0grpopts: nrdf: 18215.8 282921 ref-t: 300 300 tau-t: 0.1 0.1annealing: No Noannealing-npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[ 0]: 0 0 0 0 energygrp-flags[ 1]: 0 0 0 0 energygrp-flags[ 2]: 0 0 0 0 energygrp-flags[ 3]: 0 0 0 0
Initializing Domain Decomposition on 40 ranksDynamic load balancing: autoWill sort the charge groups at every domain (re)decompositionInitial maximum inter charge-group distances: two-body bonded interactions: 6.348 nm, Exclusion, atoms 4566 4574 multi-body bonded interactions: 6.348 nm, U-B, atoms 4566 4574Minimum cell size due to bonded interactions: 6.983 nmMaximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nmEstimated maximum distance required for P-LINCS: 0.819 nmGuess for relative PME load: 0.21Will use 32 particle-particle and 8 PME only ranksThis is a guess, check the performance at the end of the log fileUsing 8 separate PME ranks, as guessed by mdrunScaling the initial minimum size with 1/0.8 (option -dds) = 1.25Optimizing the DD grid for 32 cells with a minimum initial size of 8.728 nmThe maximum allowed number of cells is: X 1 Y 1 Z 1
-------------------------------------------------------Program gmx mdrun, VERSION 5.1.4Source code file: /home/hpc/tar/gromacs-5.1.4/src/gromacs/domdec/domdec.cpp, line: 6987
Fatal error:There is no domain decomposition for 32 ranks that is compatible with the given box and a minimum cell size of 8.72839 nmChange the number of ranks or mdrun option -rdd or -ddsLook in the log file for details on the domain decomposition Thanks in advance
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