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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- 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. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists