Hello Did you use constraints = none instead of LINCS. It could work better
bests, Emanuel >>> Bongkeun Kim 15.12.10 9.42 Uhr >>> Hello, I tried using 1fs timestep and it did not work. I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not supported gpu and I had to use "force-device=y". Do you think this is the reason of the error? Thanks. Bongkeun Kim Quoting Emanuel Peter : > Hello, > > If you use for your timestep 1fs instead of 2fs, it could run better. > > Bests, > > Emanuel > >>>> Bongkeun Kim 15.12.10 8.36 Uhr >>> > Hello, > > > > I got an error log when I used gromacs-gpu on npt simulation. > > The error is like: > > --------------------------------------------------------------- > > Input Parameters: > > integrator = md > > nsteps = 50000000 > > init_step = 0 > > ns_type = Grid > > nstlist = 5 > > ndelta = 2 > > nstcomm = 10 > > comm_mode = Linear > > nstlog = 1000 > > nstxout = 1000 > > nstvout = 1000 > > nstfout = 0 > > nstcalcenergy = 5 > > nstenergy = 1000 > > nstxtcout = 1000 > > init_t = 0 > > delta_t = 0.002 > > xtcprec = 1000 > > nkx = 32 > > nky = 32 > > nkz = 32 > > pme_order = 4 > > ewald_rtol = 1e-05 > > ewald_geometry = 0 > > epsilon_surface = 0 > > optimize_fft = FALSE > > ePBC = xyz > > bPeriodicMols = FALSE > > bContinuation = TRUE > > bShakeSOR = FALSE > > etc = V-rescale > > nsttcouple = 5 > > epc = Parrinello-Rahman > > epctype = Isotropic > > nstpcouple = 5 > > tau_p = 2 > > 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} > > compress (3x3): > > compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} > > compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} > > compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} > > 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 > > andersen_seed = 815131 > > rlist = 1 > > rlistlong = 1 > > rtpi = 0.05 > > coulombtype = PME > > rcoulomb_switch = 0 > > rcoulomb = 1 > > vdwtype = Cut-off > > rvdw_switch = 0 > > rvdw = 1 > > epsilon_r = 1 > > epsilon_rf = 1 > > tabext = 1 > > implicit_solvent = No > > gb_algorithm = Still > > gb_epsilon_solvent = 80 > > nstgbradii = 1 > > rgbradii = 1 > > 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 > > DispCorr = EnerPres > > free_energy = no > > init_lambda = 0 > > delta_lambda = 0 > > n_foreign_lambda = 0 > > sc_alpha = 0 > > sc_power = 0 > > sc_sigma = 0.3 > > sc_sigma_min = 0.3 > > nstdhdl = 10 > > separate_dhdl_file = yes > > dhdl_derivatives = yes > > dh_hist_size = 0 > > dh_hist_spacing = 0.1 > > nwall = 0 > > wall_type = 9-3 > > wall_atomtype[0] = -1 > > wall_atomtype[1] = -1 > > wall_density[0] = 0 > > wall_density[1] = 0 > > wall_ewald_zfac = 3 > > pull = no > > disre = No > > disre_weighting = Conservative > > disre_mixed = FALSE > > dr_fc = 1000 > > dr_tau = 0 > > nstdisreout = 100 > > orires_fc = 0 > > orires_tau = 0 > > nstorireout = 100 > > dihre-fc = 1000 > > em_stepsize = 0.01 > > em_tol = 10 > > niter = 20 > > fc_stepsize = 0 > > nstcgsteep = 1000 > > nbfgscorr = 10 > > ConstAlg = Lincs > > shake_tol = 0.0001 > > lincs_order = 4 > > lincs_warnangle = 30 > > lincs_iter = 1 > > bd_fric = 0 > > ld_seed = 1993 > > cos_accel = 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} > > userint1 = 0 > > userint2 = 0 > > userint3 = 0 > > userint4 = 0 > > userreal1 = 0 > > userreal2 = 0 > > userreal3 = 0 > > userreal4 = 0 > > grpopts: > > nrdf: 24715 > > ref_t: 325 > > tau_t: 0.1 > > anneal: No > > ann_npoints: 0 > > acc: 0 0 0 > > nfreeze: N N N > > energygrp_flags[ 0]: 0 > > efield-x: > > n = 0 > > efield-xt: > > n = 0 > > efield-y: > > n = 0 > > efield-yt: > > n = 0 > > efield-z: > > n = 0 > > efield-zt: > > n = 0 > > bQMMM = FALSE > > QMconstraints = 0 > > QMMMscheme = 0 > > scalefactor = 1 > > qm_opts: > > ngQM = 0 > > Table routines are used for coulomb: TRUE > > Table routines are used for vdw: FALSE > > Will do PME sum in reciprocal space. > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen > > A smooth particle mesh Ewald method > > J. Chem. Phys. 103 (1995) pp. 8577-8592 > > -------- -------- --- Thank You --- -------- -------- > > > > Will do ordinary reciprocal space Ewald sum. > > Using a Gaussian width (1/beta) of 0.320163 nm for Ewald > > Cut-off's: NS: 1 Coulomb: 1 LJ: 1 > > Long Range LJ corr.: 2.9723e-04 > > System total charge: 0.000 > > Generated table with 1000 data points for Ewald. > > Tabscale = 500 points/nm > > Generated table with 1000 data points for LJ6. > > Tabscale = 500 points/nm > > Generated table with 1000 data points for LJ12. > > Tabscale = 500 points/nm > > Generated table with 1000 data points for 1-4 COUL. > > Tabscale = 500 points/nm > > Generated table with 1000 data points for 1-4 LJ6. > > Tabscale = 500 points/nm > > Generated table with 1000 data points for 1-4 LJ12. > > Tabscale = 500 points/nm > > > > Enabling SPC-like water optimization for 3910 molecules. > > > > Configuring nonbonded kernels... > > Configuring standard C nonbonded kernels... > > > > > > > > Initializing LINear Constraint Solver > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije > > LINCS: A Linear Constraint Solver for molecular simulations > > J. Comp. Chem. 18 (1997) pp. 1463-1472 > > -------- -------- --- Thank You --- -------- -------- > > > > The number of constraints is 626 > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > S. Miyamoto and P. A. Kollman > > SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid > > Water Models > > J. Comp. Chem. 13 (1992) pp. 952-962 > > -------- -------- --- Thank You --- -------- -------- > > > > Center of mass motion removal mode is Linear > > We have the following groups for center of mass motion removal: > > 0: rest > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > G. Bussi, D. Donadio and M. Parrinello > > Canonical sampling through velocity rescaling > > J. Chem. Phys. 126 (2007) pp. 014101 > > -------- -------- --- Thank You --- -------- -------- > > > > Max number of connections per atom is 103 > > Total number of connections is 37894 > > Max number of graph edges per atom is 4 > > Total number of graph edges is 16892 > > > > OpenMM plugins loaded from directory /home/bkim/packages/openmm/lib/plugins: > > libOpenMMCuda.so, libOpenMMOpenCL.so, > > The combination rule of the used force field matches the one used by OpenMM. > > Gromacs will use the OpenMM platform: Cuda > > Non-supported GPU selected (#1, Tesla T10 Processor), forced > > continuing.Note, th > > at the simulation can be slow or it migth even crash. > > Pre-simulation ~15s memtest in progress... > > Memory test completed without errors. > > > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > > Entry Friedrichs2009 not found in citation database > > -------- -------- --- Thank You --- -------- -------- > > > > Initial temperature: 0 K > > > > Started mdrun on node 0 Tue Dec 14 23:10:20 2010 > > > > Step Time Lambda > > 0 0.00000 0.00000 > > > > Energies (kJ/mol) > > Potential Kinetic En. Total Energy Temperature Constr. rmsd > > -1.40587e+05 3.36048e+04 -1.06982e+05 3.27065e+02 0.00000e+00 > > > > Step Time Lambda > > 1000 2.00000 0.00000 > > > > Energies (kJ/mol) > > Potential Kinetic En. Total Energy Temperature Constr. rmsd > > nan nan nan nan 0.00000e+00 > > > > > > > > Received the second INT/TERM signal, stopping at the next step > > > > Step Time Lambda > > 1927 3.85400 0.00000 > > > > Energies (kJ/mol) > > Potential Kinetic En. Total Energy Temperature Constr. rmsd > > nan nan nan nan 0.00000e+00 > > > > Writing checkpoint, step 1927 at Tue Dec 14 23:12:07 2010 > > > > > > <====== ############### ==> > > <==== A V E R A G E S ====> > > <== ############### ======> > > > > Statistics over 3 steps using 3 frames > > > > Energies (kJ/mol) > > Potential Kinetic En. Total Energy Temperature Constr. rmsd > > nan nan nan nan 0.00000e+00 > > > > Box-X Box-Y Box-Z > > 3.91363e-24 6.72623e-44 -1.71925e+16 > > > > Total Virial (kJ/mol) > > 0.00000e+00 0.00000e+00 0.00000e+00 > > 0.00000e+00 0.00000e+00 0.00000e+00 > > 0.00000e+00 0.00000e+00 0.00000e+00 > > > > Pressure (bar) > > 0.00000e+00 0.00000e+00 0.00000e+00 > > 0.00000e+00 0.00000e+00 0.00000e+00 > > 0.00000e+00 0.00000e+00 0.00000e+00 > > > > Total Dipole (D) > > 0.00000e+00 0.00000e+00 0.00000e+00 > > ------------------------------------------------------------------------ > > > > The input mdp file is given by > > ======================================================== > > title = OPLS Lysozyme MD > > ; Run parameters > > integrator = md ; leap-frog integrator > > nsteps = 50000000 ; > > dt = 0.002 ; 2 fs > > ; Output control > > nstxout = 1000 ; save coordinates every 2 ps > > nstvout = 1000 ; save velocities every 2 ps > > nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps > > nstenergy = 1000 ; save energies every 2 ps > > nstlog = 1000 ; update log file every 2 ps > > ; Bond parameters > > continuation = yes ; Restarting after NPT > > constraint_algorithm = lincs ; holonomic constraints > > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > > constraine > > d > > lincs_iter = 1 ; accuracy of LINCS > > lincs_order = 4 ; also related to accuracy > > ; Neighborsearching > > ns_type = grid ; search neighboring grid cels > > nstlist = 5 ; 10 fs > > rlist = 1.0 ; short-range neighborlist cutoff (in nm) > > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) > > rvdw = 1.0 ; short-range van der Waals cutoff (in nm) > > ; Electrostatics > > coulombtype = PME ; Particle Mesh Ewald for long-range > > electrostat > > ics > > pme_order = 4 ; cubic interpolation > > fourierspacing = 0.16 ; grid spacing for FFT > > ; Temperature coupling is on > > tcoupl = V-rescale ; modified Berendsen thermostat > > tc-grps = System ; two coupling groups - more accurate > > tau_t = 0.1 ; time constant, in ps > > ref_t = 325 ; reference temperature, one for each > > group, in > > K > > ; Pressure coupling is on > > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > > pcoupltype = isotropic ; uniform scaling of box vectors > > tau_p = 2.0 ; time constant, in ps > > ref_p = 1.0 ; reference pressure, in bar > > compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 > > ; Periodic boundary conditions > > pbc = xyz ; 3-D PBC > > ; Dispersion correction > > DispCorr = EnerPres ; account for cut-off vdW scheme > > ; Velocity generation > > gen_vel = no ; Velocity generation is off > > ========================================================================= > > > > It worked with generic cpu mdrun but gave this error when mdrun-gpu > > was used by > > > > mdrun-gpu -deffnm md_0_2 -device > > "OpenMM:platform=Cuda,deviceid=1,force-device=y > > es" > > > > If you have any idea how to avoid this problem, I will really appreciate it. > > Thank you. > > Bongkeun Kim > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. 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