Hi, The beta versions are all outdated, could you please use the latest source distribution (4.5.1) instead (or git from the release-4-5-patches branch)? The instructions are here: http://www.gromacs.org/gpu#Compiling_and_custom_installation_of_GROMACS-GPU
>> The requested platform "CUDA" could not be found AFAIR that is generally the sign of a problem with the mismatch between the CUDA version of the libraries mdrun and openmm are linked against with. Let us know if you succeed! -- Szilárd >> >> >> >> The output of gmx4.5-beta2 is >> -------------------------------------------------------------------------- >> Log file opened on Mon Oct 4 21:56:10 2010 >> Host: powerpc pid: 30370 nodeid: 0 nnodes: 1 >> The Gromacs distribution was built @TMP_TIME@ by >> ros...@mohawk.cbr.su.se [CMAKE] (@TMP_MACHINE@) >> >> :-) G R O M A C S (-: >> GROwing Monsters And Cloning Shrimps >> :-) VERSION 4.5-GPU-beta2 (-: >> >> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. >> Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2008, The GROMACS development team, >> check out http://www.gromacs.org for more information. >> This program is free software; you can redistribute it and/or >> modify it under the terms of the GNU General Public License >> as published by the Free Software Foundation; either version 2 >> of the License, or (at your option) any later version. >> :-) /home/leontyev/programs/bin/gromacs/gromacs-4.5-beta2/bin/mdrun-gpu (-: >> >> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ >> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl >> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable >> molecular simulation >> J. Chem. Theory Comput. 4 (2008) pp. 435-447 >> -------- -------- --- Thank You --- -------- -------- >> >> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ >> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. >> Berendsen >> GROMACS: Fast, Flexible and Free >> J. Comp. Chem. 26 (2005) pp. 1701-1719 >> -------- -------- --- Thank You --- -------- -------- >> >> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ >> E. Lindahl and B. Hess and D. van der Spoel >> GROMACS 3.0: A package for molecular simulation and trajectory analysis >> J. Mol. Mod. 7 (2001) pp. 306-317 >> -------- -------- --- Thank You --- -------- -------- >> >> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ >> H. J. C. Berendsen, D. van der Spoel and R. van Drunen >> GROMACS: A message-passing parallel molecular dynamics implementation >> Comp. Phys. Comm. 91 (1995) pp. 43-56 >> -------- -------- --- Thank You --- -------- -------- >> Input Parameters: >> integrator = md >> nsteps = 100 >> init_step = 0 >> nstcalcenergy = 10 >> ns_type = Simple >> nstlist = 0 >> ndelta = 2 >> nstcomm = 1003 >> comm_mode = Linear >> nstlog = 10 >> nstxout = 5000 >> nstvout = 10000000 >> nstfout = 0 >> nstenergy = 1000 >> nstxtcout = 1 >> init_t = 0 >> delta_t = 0.001 >> xtcprec = 1000 >> nkx = 0 >> nky = 0 >> nkz = 0 >> pme_order = 4 >> ewald_rtol = 1e-05 >> ewald_geometry = 0 >> epsilon_surface = 0 >> optimize_fft = FALSE >> ePBC = xyz >> bPeriodicMols = FALSE >> bContinuation = FALSE >> bShakeSOR = FALSE >> etc = No >> nsttcouple = -1 >> epc = No >> epctype = Isotropic >> nstpcouple = -1 >> tau_p = 1 >> ref_p (3x3): >> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> compress (3x3): >> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} >> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+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 >> andersen_seed = 815131 >> rlist = 1 >> rlistlong = 1 >> rtpi = 0.05 >> coulombtype = Cut-off >> 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 = No >> sa_surface_tension = 2.092 >> DispCorr = No >> free_energy = no >> init_lambda = 0 >> delta_lambda = 0 >> n_foreign_lambda = 0 >> sc_alpha = 0 >> sc_power = 0 >> sc_sigma = 0.3 >> nstdhdl = 10 >> dh_table_size = 0 >> dh_table_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 = 8 >> lincs_warnangle = 30 >> lincs_iter = 4 >> 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: 99024 >> ref_t: 0 >> tau_t: 0 >> anneal: No >> ann_npoints: 0 >> acc: 0 0 0 >> nfreeze: N N N >> energygrp_flags[ 0]: 0 0 >> energygrp_flags[ 1]: 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: FALSE >> Table routines are used for vdw: FALSE >> Cut-off's: NS: 1 Coulomb: 1 LJ: 1 >> System total charge: -0.000 >> 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 11505 molecules. >> Configuring nonbonded kernels... >> Configuring standard C nonbonded kernels... >> >> Removing pbc first time >> 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 5967 >> ++++ 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 >> Max number of connections per atom is 91 >> Total number of connections is 387700 >> Max number of graph edges per atom is 6 >> Total number of graph edges is 70330 >> OpenMM plugins loaded from directory >> /home/leontyev/programs/bin/gromacs/gromacs-4.5-beta2/bin/../openmm/lib/plugins: >> libOpenMMCuda.so, >> ------------------------------------------------------- >> Program mdrun-gpu, VERSION 4.5-GPU-beta2 >> Source code file: >> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/kernel/openmm_wrapper.cpp, >> line: 550 >> Fatal error: >> OpenMM supports only the following methods for electrostatics: NoCutoff >> (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME. >> For more information and tips for troubleshooting, please check the GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ------------------------------------------------------- >> -- >> gmx-developers mailing list >> gmx-develop...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-developers >> Please don't post (un)subscribe requests to the list. Use the www interface >> or send it to gmx-developers-requ...@gromacs.org. >> > -- 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
