It doesn't work, even I deleted this line.... it stills shows the same error... I use ./mdrun-gpu without any flags. Did I miss something? YY > Date: Thu, 11 Nov 2010 20:25:45 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] ./mdrun > > > > lin hen wrote: > > > > 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? > > You haven't properly commented out the "nsteps = -1" line. The comment sign > is > a ';' not '#' though I'm surprised grompp didn't simply abort with this input > file. > > -Justin > > > > > Thanks a lot > > > > YY > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
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