constraints = all-bonds integrator = md dt = 0.002 ; ps ! #nsteps = -1 nsteps = 100 nstlist = 0 ns_type = grid rlist = 0 coulombtype = cut-off vdwtype = cut-off rcoulomb = 0 rvdw = 0 pbc = no epsilon_rf = 0 rgbradii = 0 comm_mode = angular implicit_solvent = GBSA gb_algorithm = OBC gb_epsilon_solvent = 78.3 sa_surface_tension = 2.25936 nstxout = 0 nstfout = 0 nstvout = 0 nstxtcout = 0 nstlog = 0 nstcalcenergy = -1 nstenergy = 0 tcoupl = berendsen tc-grps = system tau-t = 0.1 ref-t = 300
This is the .mdf file, even I modified the nsteps, it still comes with the same error: Back Off! I just backed up ener.edr to ./#ener.edr.1# WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol" option. WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in OpenMM with the default Gromacs values. Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'Protein' -1 steps, infinite ps. the log file: Input Parameters: integrator = md nsteps = -1 init_step = 0 ns_type = Grid nstlist = 0 ndelta = 2 nstcomm = 10 comm_mode = Angular nstlog = 0 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy = 10 nstenergy = 0 the nsteps is still -1, did I do something wrong? Thanks a lot YY From: rol...@utk.edu Date: Tue, 9 Nov 2010 21:34:34 -0500 Subject: Re: [gmx-users] ./mdrun To: gmx-users@gromacs.org Hi, as you output says. It infinite long trajectory. Either set a number of steps (in mdp file or with tpbconf) or set a maximum time with (mdrun -maxh) Roland On Tue, Nov 9, 2010 at 9:03 PM, lin hen <cutey...@live.com> wrote: Hi, I am using the dhfr gpu benchmark with mdrun-gpu:dhfr-solv-RF-2nm.bench. export LD_LIBRARY_PATH=/path to OPENMM lib and cuda lib/ export OPENMM_PLUGIN=/path to OPENMM lib plugins/ it shows: Back Off! I just backed up md.log to ./#md.log.1# Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) Back Off! I just backed up ener.edr to ./#ener.edr.1# WARNING: OpenMM does not support leap-frog, will use velocity-verlet integrator. WARNING: OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators. WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol" option. Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'Protein in water' -1 steps, infinite ps. and keeps this status for at least one hour, did I miss something? or do somthing wrong? thanks, yy -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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