<html><head><meta http-equiv=Content-Type content="text/html; charset=ks_c_5601-1987"><META name="Author" content="Novell GroupWise WebAccess"></head><body style='font-family: Tahoma, sans-serif; font-size: 13px; '>Hello,<br><br>If you use for your timestep 1fs instead of 2fs, it could run better.<br><br>Bests,<br><br>Emanuel <br><br>>>> Bongkeun Kim <bkim@chem.ucsb.edu> 15.12.10 8.36 Uhr >>><br>Hello,<br><br><br><br>I got an error log when I used gromacs-gpu on npt simulation.<br><br>The error is like:<br><br>---------------------------------------------------------------<br><br>Input Parameters:<br><br> integrator = md<br><br> nsteps = 50000000<br><br> init_step = 0<br><br> ns_type = Grid<br><br> nstlist = 5<br><br> ndelta = 2<br><br> nstcomm = 10<br><br> comm_mode = Linear<br><br> nstlog = 1000<br><br> nstxout = 1000<br><br> nstvout = 1000<br><br> nstfout = 0<br><br> nstcalcenergy = 5<br><br> nstenergy = 1000<br><br> nstxtcout = 1000<br><br> init_t = 0<br><br> delta_t = 0.002<br><br> xtcprec = 1000<br><br> nkx = 32<br><br> nky = 32<br><br> nkz = 32<br><br> pme_order = 4<br><br> ewald_rtol = 1e-05<br><br> ewald_geometry = 0<br><br> epsilon_surface = 0<br><br> optimize_fft = FALSE<br><br> ePBC = xyz<br><br> bPeriodicMols = FALSE<br><br> bContinuation = TRUE<br><br> bShakeSOR = FALSE<br><br> etc = V-rescale<br><br> nsttcouple = 5<br><br> epc = Parrinello-Rahman<br><br> epctype = Isotropic<br><br> nstpcouple = 5<br><br> tau_p = 2<br><br> ref_p (3x3):<br><br> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}<br><br> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}<br><br> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}<br><br> compress (3x3):<br><br> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}<br><br> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}<br><br> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}<br><br> refcoord_scaling = No<br><br> posres_com (3):<br><br> posres_com[0]= 0.00000e+00<br><br> posres_com[1]= 0.00000e+00<br><br> posres_com[2]= 0.00000e+00<br><br> posres_comB (3):<br><br> posres_comB[0]= 0.00000e+00<br><br> posres_comB[1]= 0.00000e+00<br><br> posres_comB[2]= 0.00000e+00<br><br> andersen_seed = 815131<br><br> rlist = 1<br><br> rlistlong = 1<br><br> rtpi = 0.05<br><br> coulombtype = PME<br><br> rcoulomb_switch = 0<br><br> rcoulomb = 1<br><br> vdwtype = Cut-off<br><br> rvdw_switch = 0<br><br> rvdw = 1<br><br> epsilon_r = 1<br><br> epsilon_rf = 1<br><br> tabext = 1<br><br> implicit_solvent = No<br><br> gb_algorithm = Still<br><br> gb_epsilon_solvent = 80<br><br> nstgbradii = 1<br><br> rgbradii = 1<br><br> gb_saltconc = 0<br><br> gb_obc_alpha = 1<br><br> gb_obc_beta = 0.8<br><br> gb_obc_gamma = 4.85<br><br> gb_dielectric_offset = 0.009<br><br> sa_algorithm = Ace-approximation<br><br> sa_surface_tension = 2.05016<br><br> DispCorr = EnerPres<br><br> free_energy = no<br><br> init_lambda = 0<br><br> delta_lambda = 0<br><br> n_foreign_lambda = 0<br><br> sc_alpha = 0<br><br> sc_power = 0<br><br> sc_sigma = 0.3<br><br> sc_sigma_min = 0.3<br><br> nstdhdl = 10<br><br> separate_dhdl_file = yes<br><br> dhdl_derivatives = yes<br><br> dh_hist_size = 0<br><br> dh_hist_spacing = 0.1<br><br> nwall = 0<br><br> wall_type = 9-3<br><br> wall_atomtype[0] = -1<br><br> wall_atomtype[1] = -1<br><br> wall_density[0] = 0<br><br> wall_density[1] = 0<br><br> wall_ewald_zfac = 3<br><br> pull = no<br><br> disre = No<br><br> disre_weighting = Conservative<br><br> disre_mixed = FALSE<br><br> dr_fc = 1000<br><br> dr_tau = 0<br><br> nstdisreout = 100<br><br> orires_fc = 0<br><br> orires_tau = 0<br><br> nstorireout = 100<br><br> dihre-fc = 1000<br><br> em_stepsize = 0.01<br><br> em_tol = 10<br><br> niter = 20<br><br> fc_stepsize = 0<br><br> nstcgsteep = 1000<br><br> nbfgscorr = 10<br><br> ConstAlg = Lincs<br><br> shake_tol = 0.0001<br><br> lincs_order = 4<br><br> lincs_warnangle = 30<br><br> lincs_iter = 1<br><br> bd_fric = 0<br><br> ld_seed = 1993<br><br> cos_accel = 0<br><br> deform (3x3):<br><br> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br><br> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br><br> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br><br> userint1 = 0<br><br> userint2 = 0<br><br> userint3 = 0<br><br> userint4 = 0<br><br> userreal1 = 0<br><br> userreal2 = 0<br><br> userreal3 = 0<br><br> userreal4 = 0<br><br>grpopts:<br><br> nrdf: 24715<br><br> ref_t: 325<br><br> tau_t: 0.1<br><br>anneal: No<br><br>ann_npoints: 0<br><br> acc: 0 0 0<br><br> nfreeze: N N N<br><br> energygrp_flags[ 0]: 0<br><br> efield-x:<br><br> n = 0<br><br> efield-xt:<br><br> n = 0<br><br> efield-y:<br><br> n = 0<br><br> efield-yt:<br><br> n = 0<br><br> efield-z:<br><br> n = 0<br><br> efield-zt:<br><br> n = 0<br><br> bQMMM = FALSE<br><br> QMconstraints = 0<br><br> QMMMscheme = 0<br><br> scalefactor = 1<br><br>qm_opts:<br><br> ngQM = 0<br><br>Table routines are used for coulomb: TRUE<br><br>Table routines are used for vdw: FALSE<br><br>Will do PME sum in reciprocal space.<br><br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen<br><br>A smooth particle mesh Ewald method<br><br>J. Chem. Phys. 103 (1995) pp. 8577-8592<br><br>-------- -------- --- Thank You --- -------- --------<br><br><br><br>Will do ordinary reciprocal space Ewald sum.<br><br>Using a Gaussian width (1/beta) of 0.320163 nm for Ewald<br><br>Cut-off's: NS: 1 Coulomb: 1 LJ: 1<br><br>Long Range LJ corr.: <C6> 2.9723e-04<br><br>System total charge: 0.000<br><br>Generated table with 1000 data points for Ewald.<br><br>Tabscale = 500 points/nm<br><br>Generated table with 1000 data points for LJ6.<br><br>Tabscale = 500 points/nm<br><br>Generated table with 1000 data points for LJ12.<br><br>Tabscale = 500 points/nm<br><br>Generated table with 1000 data points for 1-4 COUL.<br><br>Tabscale = 500 points/nm<br><br>Generated table with 1000 data points for 1-4 LJ6.<br><br>Tabscale = 500 points/nm<br><br>Generated table with 1000 data points for 1-4 LJ12.<br><br>Tabscale = 500 points/nm<br><br><br><br>Enabling SPC-like water optimization for 3910 molecules.<br><br><br><br>Configuring nonbonded kernels...<br><br>Configuring standard C nonbonded kernels...<br><br><br><br><br><br><br><br>Initializing LINear Constraint Solver<br><br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije<br><br>LINCS: A Linear Constraint Solver for molecular simulations<br><br>J. Comp. Chem. 18 (1997) pp. 1463-1472<br><br>-------- -------- --- Thank You --- -------- --------<br><br><br><br>The number of constraints is 626<br><br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>S. Miyamoto and P. A. Kollman<br><br>SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid<br><br>Water Models<br><br>J. Comp. Chem. 13 (1992) pp. 952-962<br><br>-------- -------- --- Thank You --- -------- --------<br><br><br><br>Center of mass motion removal mode is Linear<br><br>We have the following groups for center of mass motion removal:<br><br> 0: rest<br><br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>G. Bussi, D. Donadio and M. Parrinello<br><br>Canonical sampling through velocity rescaling<br><br>J. Chem. Phys. 126 (2007) pp. 014101<br><br>-------- -------- --- Thank You --- -------- --------<br><br><br><br>Max number of connections per atom is 103<br><br>Total number of connections is 37894<br><br>Max number of graph edges per atom is 4<br><br>Total number of graph edges is 16892<br><br><br><br>OpenMM plugins loaded from directory /home/bkim/packages/openmm/lib/plugins:<br><br>libOpenMMCuda.so, libOpenMMOpenCL.so,<br><br>The combination rule of the used force field matches the one used by OpenMM.<br><br>Gromacs will use the OpenMM platform: Cuda<br><br>Non-supported GPU selected (#1, Tesla T10 Processor), forced <br><br>continuing.Note, th<br><br>at the simulation can be slow or it migth even crash.<br><br>Pre-simulation ~15s memtest in progress...<br><br>Memory test completed without errors.<br><br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>Entry Friedrichs2009 not found in citation database<br><br>-------- -------- --- Thank You --- -------- --------<br><br><br><br>Initial temperature: 0 K<br><br><br><br>Started mdrun on node 0 Tue Dec 14 23:10:20 2010<br><br><br><br> Step Time Lambda<br><br> 0 0.00000 0.00000<br><br><br><br> Energies (kJ/mol)<br><br> Potential Kinetic En. Total Energy Temperature Constr. rmsd<br><br> -1.40587e+05 3.36048e+04 -1.06982e+05 3.27065e+02 0.00000e+00<br><br><br><br> Step Time Lambda<br><br> 1000 2.00000 0.00000<br><br><br><br> Energies (kJ/mol)<br><br> Potential Kinetic En. Total Energy Temperature Constr. rmsd<br><br> nan nan nan nan 0.00000e+00<br><br><br><br><br><br><br><br>Received the second INT/TERM signal, stopping at the next step<br><br><br><br> Step Time Lambda<br><br> 1927 3.85400 0.00000<br><br><br><br> Energies (kJ/mol)<br><br> Potential Kinetic En. Total Energy Temperature Constr. rmsd<br><br> nan nan nan nan 0.00000e+00<br><br><br><br>Writing checkpoint, step 1927 at Tue Dec 14 23:12:07 2010<br><br><br><br><br><br> <====== ############### ==><br><br> <==== A V E R A G E S ====><br><br> <== ############### ======><br><br><br><br> Statistics over 3 steps using 3 frames<br><br><br><br> Energies (kJ/mol)<br><br> Potential Kinetic En. Total Energy Temperature Constr. rmsd<br><br> nan nan nan nan 0.00000e+00<br><br><br><br> Box-X Box-Y Box-Z<br><br> 3.91363e-24 6.72623e-44 -1.71925e+16<br><br><br><br> Total Virial (kJ/mol)<br><br> 0.00000e+00 0.00000e+00 0.00000e+00<br><br> 0.00000e+00 0.00000e+00 0.00000e+00<br><br> 0.00000e+00 0.00000e+00 0.00000e+00<br><br><br><br> Pressure (bar)<br><br> 0.00000e+00 0.00000e+00 0.00000e+00<br><br> 0.00000e+00 0.00000e+00 0.00000e+00<br><br> 0.00000e+00 0.00000e+00 0.00000e+00<br><br><br><br> Total Dipole (D)<br><br> 0.00000e+00 0.00000e+00 0.00000e+00<br><br>------------------------------------------------------------------------<br><br><br><br>The input mdp file is given by<br><br>========================================================<br><br>title = OPLS Lysozyme MD<br><br>; Run parameters<br><br>integrator = md ; leap-frog integrator<br><br>nsteps = 50000000 ;<br><br>dt = 0.002 ; 2 fs<br><br>; Output control<br><br>nstxout = 1000 ; save coordinates every 2 ps<br><br>nstvout = 1000 ; save velocities every 2 ps<br><br>nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps<br><br>nstenergy = 1000 ; save energies every 2 ps<br><br>nstlog = 1000 ; update log file every 2 ps<br><br>; Bond parameters<br><br>continuation = yes ; Restarting after NPT<br><br>constraint_algorithm = lincs ; holonomic constraints<br><br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) <br><br>constraine<br><br>d<br><br>lincs_iter = 1 ; accuracy of LINCS<br><br>lincs_order = 4 ; also related to accuracy<br><br>; Neighborsearching<br><br>ns_type = grid ; search neighboring grid cels<br><br>nstlist = 5 ; 10 fs<br><br>rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br><br>rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br><br>rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br><br>; Electrostatics<br><br>coulombtype = PME ; Particle Mesh Ewald for long-range <br><br>electrostat<br><br>ics<br><br>pme_order = 4 ; cubic interpolation<br><br>fourierspacing = 0.16 ; grid spacing for FFT<br><br>; Temperature coupling is on<br><br>tcoupl = V-rescale ; modified Berendsen thermostat<br><br>tc-grps = System ; two coupling groups - more accurate<br><br>tau_t = 0.1 ; time constant, in ps<br><br>ref_t = 325 ; reference temperature, one for each <br><br>group, in<br><br>K<br><br>; Pressure coupling is on<br><br>pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br><br>pcoupltype = isotropic ; uniform scaling of box vectors<br><br>tau_p = 2.0 ; time constant, in ps<br><br>ref_p = 1.0 ; reference pressure, in bar<br><br>compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1<br><br>; Periodic boundary conditions<br><br>pbc = xyz ; 3-D PBC<br><br>; Dispersion correction<br><br>DispCorr = EnerPres ; account for cut-off vdW scheme<br><br>; Velocity generation<br><br>gen_vel = no ; Velocity generation is off<br><br>=========================================================================<br><br><br><br>It worked with generic cpu mdrun but gave this error when mdrun-gpu <br><br>was used by<br><br><br><br>mdrun-gpu -deffnm md_0_2 -device <br><br>"OpenMM:platform=Cuda,deviceid=1,force-device=y<br><br>es"<br><br><br><br>If you have any idea how to avoid this problem, I will really appreciate it.<br><br>Thank you.<br><br>Bongkeun Kim<br><br><br><br><br><br>-- <br><br>gmx-users mailing list gmx-users@gromacs.org<br><br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br><br>Please don't post (un)subscribe requests to the list. 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