<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>Did you use constraints = none instead of LINCS.<br>It could work better<br><br>bests,<br><br>Emanuel<br><br>>>> Bongkeun Kim <bkim@chem.ucsb.edu> 15.12.10 9.42 Uhr >>><br>Hello,<br><br><br><br>I tried using 1fs timestep and it did not work.<br><br>I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not <br><br>supported gpu and I had to use "force-device=y". Do you think this is <br><br>the reason of the error?<br><br>Thanks.<br><br>Bongkeun Kim<br><br><br><br>Quoting Emanuel Peter <Emanuel.Peter@chemie.uni-regensburg.de>:<br><br><br><br>> Hello,<br><br>><br><br>> If you use for your timestep 1fs instead of 2fs, it could run better.<br><br>><br><br>> Bests,<br><br>><br><br>> Emanuel<br><br>><br><br>>>>> Bongkeun Kim 15.12.10 8.36 Uhr >>><br><br>> Hello,<br><br>><br><br>><br><br>><br><br>> I got an error log when I used gromacs-gpu on npt simulation.<br><br>><br><br>> The error is like:<br><br>><br><br>> ---------------------------------------------------------------<br><br>><br><br>> Input Parameters:<br><br>><br><br>> integrator = md<br><br>><br><br>> nsteps = 50000000<br><br>><br><br>> init_step = 0<br><br>><br><br>> ns_type = Grid<br><br>><br><br>> nstlist = 5<br><br>><br><br>> ndelta = 2<br><br>><br><br>> nstcomm = 10<br><br>><br><br>> comm_mode = Linear<br><br>><br><br>> nstlog = 1000<br><br>><br><br>> nstxout = 1000<br><br>><br><br>> nstvout = 1000<br><br>><br><br>> nstfout = 0<br><br>><br><br>> nstcalcenergy = 5<br><br>><br><br>> nstenergy = 1000<br><br>><br><br>> nstxtcout = 1000<br><br>><br><br>> init_t = 0<br><br>><br><br>> delta_t = 0.002<br><br>><br><br>> xtcprec = 1000<br><br>><br><br>> nkx = 32<br><br>><br><br>> nky = 32<br><br>><br><br>> nkz = 32<br><br>><br><br>> pme_order = 4<br><br>><br><br>> ewald_rtol = 1e-05<br><br>><br><br>> ewald_geometry = 0<br><br>><br><br>> epsilon_surface = 0<br><br>><br><br>> optimize_fft = FALSE<br><br>><br><br>> ePBC = xyz<br><br>><br><br>> bPeriodicMols = FALSE<br><br>><br><br>> bContinuation = TRUE<br><br>><br><br>> bShakeSOR = FALSE<br><br>><br><br>> etc = V-rescale<br><br>><br><br>> nsttcouple = 5<br><br>><br><br>> epc = Parrinello-Rahman<br><br>><br><br>> epctype = Isotropic<br><br>><br><br>> nstpcouple = 5<br><br>><br><br>> tau_p = 2<br><br>><br><br>> ref_p (3x3):<br><br>><br><br>> ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}<br><br>><br><br>> ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}<br><br>><br><br>> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}<br><br>><br><br>> compress (3x3):<br><br>><br><br>> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}<br><br>><br><br>> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}<br><br>><br><br>> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}<br><br>><br><br>> refcoord_scaling = No<br><br>><br><br>> posres_com (3):<br><br>><br><br>> posres_com[0]= 0.00000e+00<br><br>><br><br>> posres_com[1]= 0.00000e+00<br><br>><br><br>> posres_com[2]= 0.00000e+00<br><br>><br><br>> posres_comB (3):<br><br>><br><br>> posres_comB[0]= 0.00000e+00<br><br>><br><br>> posres_comB[1]= 0.00000e+00<br><br>><br><br>> posres_comB[2]= 0.00000e+00<br><br>><br><br>> andersen_seed = 815131<br><br>><br><br>> rlist = 1<br><br>><br><br>> rlistlong = 1<br><br>><br><br>> rtpi = 0.05<br><br>><br><br>> coulombtype = PME<br><br>><br><br>> rcoulomb_switch = 0<br><br>><br><br>> rcoulomb = 1<br><br>><br><br>> vdwtype = Cut-off<br><br>><br><br>> rvdw_switch = 0<br><br>><br><br>> rvdw = 1<br><br>><br><br>> epsilon_r = 1<br><br>><br><br>> epsilon_rf = 1<br><br>><br><br>> tabext = 1<br><br>><br><br>> implicit_solvent = No<br><br>><br><br>> gb_algorithm = Still<br><br>><br><br>> gb_epsilon_solvent = 80<br><br>><br><br>> nstgbradii = 1<br><br>><br><br>> rgbradii = 1<br><br>><br><br>> gb_saltconc = 0<br><br>><br><br>> gb_obc_alpha = 1<br><br>><br><br>> gb_obc_beta = 0.8<br><br>><br><br>> gb_obc_gamma = 4.85<br><br>><br><br>> gb_dielectric_offset = 0.009<br><br>><br><br>> sa_algorithm = Ace-approximation<br><br>><br><br>> sa_surface_tension = 2.05016<br><br>><br><br>> DispCorr = EnerPres<br><br>><br><br>> free_energy = no<br><br>><br><br>> init_lambda = 0<br><br>><br><br>> delta_lambda = 0<br><br>><br><br>> n_foreign_lambda = 0<br><br>><br><br>> sc_alpha = 0<br><br>><br><br>> sc_power = 0<br><br>><br><br>> sc_sigma = 0.3<br><br>><br><br>> sc_sigma_min = 0.3<br><br>><br><br>> nstdhdl = 10<br><br>><br><br>> separate_dhdl_file = yes<br><br>><br><br>> dhdl_derivatives = yes<br><br>><br><br>> dh_hist_size = 0<br><br>><br><br>> dh_hist_spacing = 0.1<br><br>><br><br>> nwall = 0<br><br>><br><br>> wall_type = 9-3<br><br>><br><br>> wall_atomtype[0] = -1<br><br>><br><br>> wall_atomtype[1] = -1<br><br>><br><br>> wall_density[0] = 0<br><br>><br><br>> wall_density[1] = 0<br><br>><br><br>> wall_ewald_zfac = 3<br><br>><br><br>> pull = no<br><br>><br><br>> disre = No<br><br>><br><br>> disre_weighting = Conservative<br><br>><br><br>> disre_mixed = FALSE<br><br>><br><br>> dr_fc = 1000<br><br>><br><br>> dr_tau = 0<br><br>><br><br>> nstdisreout = 100<br><br>><br><br>> orires_fc = 0<br><br>><br><br>> orires_tau = 0<br><br>><br><br>> nstorireout = 100<br><br>><br><br>> dihre-fc = 1000<br><br>><br><br>> em_stepsize = 0.01<br><br>><br><br>> em_tol = 10<br><br>><br><br>> niter = 20<br><br>><br><br>> fc_stepsize = 0<br><br>><br><br>> nstcgsteep = 1000<br><br>><br><br>> nbfgscorr = 10<br><br>><br><br>> ConstAlg = Lincs<br><br>><br><br>> shake_tol = 0.0001<br><br>><br><br>> lincs_order = 4<br><br>><br><br>> lincs_warnangle = 30<br><br>><br><br>> lincs_iter = 1<br><br>><br><br>> bd_fric = 0<br><br>><br><br>> ld_seed = 1993<br><br>><br><br>> cos_accel = 0<br><br>><br><br>> deform (3x3):<br><br>><br><br>> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br><br>><br><br>> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br><br>><br><br>> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br><br>><br><br>> userint1 = 0<br><br>><br><br>> userint2 = 0<br><br>><br><br>> userint3 = 0<br><br>><br><br>> userint4 = 0<br><br>><br><br>> userreal1 = 0<br><br>><br><br>> userreal2 = 0<br><br>><br><br>> userreal3 = 0<br><br>><br><br>> userreal4 = 0<br><br>><br><br>> grpopts:<br><br>><br><br>> nrdf: 24715<br><br>><br><br>> ref_t: 325<br><br>><br><br>> tau_t: 0.1<br><br>><br><br>> anneal: No<br><br>><br><br>> ann_npoints: 0<br><br>><br><br>> acc: 0 0 0<br><br>><br><br>> nfreeze: N N N<br><br>><br><br>> energygrp_flags[ 0]: 0<br><br>><br><br>> efield-x:<br><br>><br><br>> n = 0<br><br>><br><br>> efield-xt:<br><br>><br><br>> n = 0<br><br>><br><br>> efield-y:<br><br>><br><br>> n = 0<br><br>><br><br>> efield-yt:<br><br>><br><br>> n = 0<br><br>><br><br>> efield-z:<br><br>><br><br>> n = 0<br><br>><br><br>> efield-zt:<br><br>><br><br>> n = 0<br><br>><br><br>> bQMMM = FALSE<br><br>><br><br>> QMconstraints = 0<br><br>><br><br>> QMMMscheme = 0<br><br>><br><br>> scalefactor = 1<br><br>><br><br>> qm_opts:<br><br>><br><br>> ngQM = 0<br><br>><br><br>> Table routines are used for coulomb: TRUE<br><br>><br><br>> Table routines are used for vdw: FALSE<br><br>><br><br>> Will do PME sum in reciprocal space.<br><br>><br><br>><br><br>><br><br>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>><br><br>> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen<br><br>><br><br>> A smooth particle mesh Ewald method<br><br>><br><br>> J. Chem. Phys. 103 (1995) pp. 8577-8592<br><br>><br><br>> -------- -------- --- Thank You --- -------- --------<br><br>><br><br>><br><br>><br><br>> Will do ordinary reciprocal space Ewald sum.<br><br>><br><br>> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald<br><br>><br><br>> Cut-off's: NS: 1 Coulomb: 1 LJ: 1<br><br>><br><br>> Long Range LJ corr.: 2.9723e-04<br><br>><br><br>> System total charge: 0.000<br><br>><br><br>> Generated table with 1000 data points for Ewald.<br><br>><br><br>> Tabscale = 500 points/nm<br><br>><br><br>> Generated table with 1000 data points for LJ6.<br><br>><br><br>> Tabscale = 500 points/nm<br><br>><br><br>> Generated table with 1000 data points for LJ12.<br><br>><br><br>> Tabscale = 500 points/nm<br><br>><br><br>> Generated table with 1000 data points for 1-4 COUL.<br><br>><br><br>> Tabscale = 500 points/nm<br><br>><br><br>> Generated table with 1000 data points for 1-4 LJ6.<br><br>><br><br>> Tabscale = 500 points/nm<br><br>><br><br>> Generated table with 1000 data points for 1-4 LJ12.<br><br>><br><br>> Tabscale = 500 points/nm<br><br>><br><br>><br><br>><br><br>> Enabling SPC-like water optimization for 3910 molecules.<br><br>><br><br>><br><br>><br><br>> Configuring nonbonded kernels...<br><br>><br><br>> Configuring standard C nonbonded kernels...<br><br>><br><br>><br><br>><br><br>><br><br>><br><br>><br><br>><br><br>> Initializing LINear Constraint Solver<br><br>><br><br>><br><br>><br><br>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>><br><br>> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije<br><br>><br><br>> LINCS: A Linear Constraint Solver for molecular simulations<br><br>><br><br>> J. Comp. Chem. 18 (1997) pp. 1463-1472<br><br>><br><br>> -------- -------- --- Thank You --- -------- --------<br><br>><br><br>><br><br>><br><br>> The number of constraints is 626<br><br>><br><br>><br><br>><br><br>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>><br><br>> S. Miyamoto and P. A. Kollman<br><br>><br><br>> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid<br><br>><br><br>> Water Models<br><br>><br><br>> J. Comp. Chem. 13 (1992) pp. 952-962<br><br>><br><br>> -------- -------- --- Thank You --- -------- --------<br><br>><br><br>><br><br>><br><br>> Center of mass motion removal mode is Linear<br><br>><br><br>> We have the following groups for center of mass motion removal:<br><br>><br><br>> 0: rest<br><br>><br><br>><br><br>><br><br>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>><br><br>> G. Bussi, D. Donadio and M. Parrinello<br><br>><br><br>> Canonical sampling through velocity rescaling<br><br>><br><br>> J. Chem. Phys. 126 (2007) pp. 014101<br><br>><br><br>> -------- -------- --- Thank You --- -------- --------<br><br>><br><br>><br><br>><br><br>> Max number of connections per atom is 103<br><br>><br><br>> Total number of connections is 37894<br><br>><br><br>> Max number of graph edges per atom is 4<br><br>><br><br>> Total number of graph edges is 16892<br><br>><br><br>><br><br>><br><br>> OpenMM plugins loaded from directory /home/bkim/packages/openmm/lib/plugins:<br><br>><br><br>> libOpenMMCuda.so, libOpenMMOpenCL.so,<br><br>><br><br>> The combination rule of the used force field matches the one used by OpenMM.<br><br>><br><br>> Gromacs will use the OpenMM platform: Cuda<br><br>><br><br>> Non-supported GPU selected (#1, Tesla T10 Processor), forced<br><br>><br><br>> continuing.Note, th<br><br>><br><br>> at the simulation can be slow or it migth even crash.<br><br>><br><br>> Pre-simulation ~15s memtest in progress...<br><br>><br><br>> Memory test completed without errors.<br><br>><br><br>><br><br>><br><br>> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br><br>><br><br>> Entry Friedrichs2009 not found in citation database<br><br>><br><br>> -------- -------- --- Thank You --- -------- --------<br><br>><br><br>><br><br>><br><br>> Initial temperature: 0 K<br><br>><br><br>><br><br>><br><br>> Started mdrun on node 0 Tue Dec 14 23:10:20 2010<br><br>><br><br>><br><br>><br><br>> Step Time Lambda<br><br>><br><br>> 0 0.00000 0.00000<br><br>><br><br>><br><br>><br><br>> Energies (kJ/mol)<br><br>><br><br>> Potential Kinetic En. Total Energy Temperature Constr. rmsd<br><br>><br><br>> -1.40587e+05 3.36048e+04 -1.06982e+05 3.27065e+02 0.00000e+00<br><br>><br><br>><br><br>><br><br>> Step Time Lambda<br><br>><br><br>> 1000 2.00000 0.00000<br><br>><br><br>><br><br>><br><br>> Energies (kJ/mol)<br><br>><br><br>> Potential Kinetic En. Total Energy Temperature Constr. rmsd<br><br>><br><br>> nan nan nan nan 0.00000e+00<br><br>><br><br>><br><br>><br><br>><br><br>><br><br>><br><br>><br><br>> Received the second INT/TERM signal, stopping at the next step<br><br>><br><br>><br><br>><br><br>> Step Time Lambda<br><br>><br><br>> 1927 3.85400 0.00000<br><br>><br><br>><br><br>><br><br>> Energies (kJ/mol)<br><br>><br><br>> Potential Kinetic En. Total Energy Temperature Constr. rmsd<br><br>><br><br>> nan nan nan nan 0.00000e+00<br><br>><br><br>><br><br>><br><br>> Writing checkpoint, step 1927 at Tue Dec 14 23:12:07 2010<br><br>><br><br>><br><br>><br><br>><br><br>><br><br>> <====== ############### ==><br><br>><br><br>> <==== A V E R A G E S ====><br><br>><br><br>> <== ############### ======><br><br>><br><br>><br><br>><br><br>> Statistics over 3 steps using 3 frames<br><br>><br><br>><br><br>><br><br>> Energies (kJ/mol)<br><br>><br><br>> Potential Kinetic En. Total Energy Temperature Constr. rmsd<br><br>><br><br>> nan nan nan nan 0.00000e+00<br><br>><br><br>><br><br>><br><br>> Box-X Box-Y Box-Z<br><br>><br><br>> 3.91363e-24 6.72623e-44 -1.71925e+16<br><br>><br><br>><br><br>><br><br>> Total Virial (kJ/mol)<br><br>><br><br>> 0.00000e+00 0.00000e+00 0.00000e+00<br><br>><br><br>> 0.00000e+00 0.00000e+00 0.00000e+00<br><br>><br><br>> 0.00000e+00 0.00000e+00 0.00000e+00<br><br>><br><br>><br><br>><br><br>> Pressure (bar)<br><br>><br><br>> 0.00000e+00 0.00000e+00 0.00000e+00<br><br>><br><br>> 0.00000e+00 0.00000e+00 0.00000e+00<br><br>><br><br>> 0.00000e+00 0.00000e+00 0.00000e+00<br><br>><br><br>><br><br>><br><br>> Total Dipole (D)<br><br>><br><br>> 0.00000e+00 0.00000e+00 0.00000e+00<br><br>><br><br>> ------------------------------------------------------------------------<br><br>><br><br>><br><br>><br><br>> The input mdp file is given by<br><br>><br><br>> ========================================================<br><br>><br><br>> title = OPLS Lysozyme MD<br><br>><br><br>> ; Run parameters<br><br>><br><br>> integrator = md ; leap-frog integrator<br><br>><br><br>> nsteps = 50000000 ;<br><br>><br><br>> dt = 0.002 ; 2 fs<br><br>><br><br>> ; Output control<br><br>><br><br>> nstxout = 1000 ; save coordinates every 2 ps<br><br>><br><br>> nstvout = 1000 ; save velocities every 2 ps<br><br>><br><br>> nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps<br><br>><br><br>> nstenergy = 1000 ; save energies every 2 ps<br><br>><br><br>> nstlog = 1000 ; update log file every 2 ps<br><br>><br><br>> ; Bond parameters<br><br>><br><br>> continuation = yes ; Restarting after NPT<br><br>><br><br>> constraint_algorithm = lincs ; holonomic constraints<br><br>><br><br>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)<br><br>><br><br>> constraine<br><br>><br><br>> d<br><br>><br><br>> lincs_iter = 1 ; accuracy of LINCS<br><br>><br><br>> lincs_order = 4 ; also related to accuracy<br><br>><br><br>> ; Neighborsearching<br><br>><br><br>> ns_type = grid ; search neighboring grid cels<br><br>><br><br>> nstlist = 5 ; 10 fs<br><br>><br><br>> rlist = 1.0 ; short-range neighborlist cutoff (in nm)<br><br>><br><br>> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)<br><br>><br><br>> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)<br><br>><br><br>> ; Electrostatics<br><br>><br><br>> coulombtype = PME ; Particle Mesh Ewald for long-range<br><br>><br><br>> electrostat<br><br>><br><br>> ics<br><br>><br><br>> pme_order = 4 ; cubic interpolation<br><br>><br><br>> fourierspacing = 0.16 ; grid spacing for FFT<br><br>><br><br>> ; Temperature coupling is on<br><br>><br><br>> tcoupl = V-rescale ; modified Berendsen thermostat<br><br>><br><br>> tc-grps = System ; two coupling groups - more accurate<br><br>><br><br>> tau_t = 0.1 ; time constant, in ps<br><br>><br><br>> ref_t = 325 ; reference temperature, one for each<br><br>><br><br>> group, in<br><br>><br><br>> K<br><br>><br><br>> ; Pressure coupling is on<br><br>><br><br>> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br><br>><br><br>> pcoupltype = isotropic ; uniform scaling of box vectors<br><br>><br><br>> tau_p = 2.0 ; time constant, in ps<br><br>><br><br>> ref_p = 1.0 ; reference pressure, in bar<br><br>><br><br>> compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1<br><br>><br><br>> ; Periodic boundary conditions<br><br>><br><br>> pbc = xyz ; 3-D PBC<br><br>><br><br>> ; Dispersion correction<br><br>><br><br>> DispCorr = EnerPres ; account for cut-off vdW scheme<br><br>><br><br>> ; Velocity generation<br><br>><br><br>> gen_vel = no ; Velocity generation is off<br><br>><br><br>> =========================================================================<br><br>><br><br>><br><br>><br><br>> It worked with generic cpu mdrun but gave this error when mdrun-gpu<br><br>><br><br>> was used by<br><br>><br><br>><br><br>><br><br>> mdrun-gpu -deffnm md_0_2 -device<br><br>><br><br>> "OpenMM:platform=Cuda,deviceid=1,force-device=y<br><br>><br><br>> es"<br><br>><br><br>><br><br>><br><br>> If you have any idea how to avoid this problem, I will really appreciate it.<br><br>><br><br>> Thank you.<br><br>><br><br>> Bongkeun Kim<br><br>><br><br>><br><br>><br><br>><br><br>><br><br>> --<br><br>><br><br>> gmx-users mailing list gmx-users@gromacs.org<br><br>><br><br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br><br>><br><br>> Please search the archive at <br><br>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br><br>><br><br>> Please don't post (un)subscribe requests to the list. Use the<br><br>><br><br>> www interface or send it to gmx-users-request@gromacs.org.<br><br>><br><br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br><br>><br><br>><br><br>><br><br><br><br><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. Use the <br><br>www interface or send it to gmx-users-request@gromacs.org.<br><br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br><br></body></html>