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It doesn't work, even I deleted this line....<BR>
it stills shows the same error...<BR>
<BR>
I use ./mdrun-gpu without any flags. Did I miss something?<BR>
<BR>
YY <BR>
> Date: Thu, 11 Nov 2010 20:25:45 -0500<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] ./mdrun<BR>> <BR>> <BR>> <BR>> lin hen wrote:<BR>> > <BR>> > constraints = all-bonds<BR>> > integrator = md<BR>> > dt = 0.002 ; ps !<BR>> > #nsteps = -1<BR>> > nsteps = 100<BR>> > nstlist = 0<BR>> > ns_type = grid<BR>> > rlist = 0<BR>> > coulombtype = cut-off<BR>> > vdwtype = cut-off<BR>> > rcoulomb = 0<BR>> > rvdw = 0<BR>> > pbc = no<BR>> > epsilon_rf = 0<BR>> > rgbradii = 0<BR>> > comm_mode = angular<BR>> > implicit_solvent = GBSA<BR>> > gb_algorithm = OBC<BR>> > gb_epsilon_solvent = 78.3<BR>> > sa_surface_tension = 2.25936<BR>> > nstxout = 0<BR>> > nstfout = 0<BR>> > nstvout = 0<BR>> > nstxtcout = 0<BR>> > nstlog = 0<BR>> > nstcalcenergy = -1<BR>> > nstenergy = 0<BR>> > tcoupl = berendsen<BR>> > tc-grps = system<BR>> > tau-t = 0.1<BR>> > ref-t = 300<BR>> > <BR>> > This is the .mdf file, even I modified the nsteps, it still comes with <BR>> > the same error:<BR>> > <BR>> > Back Off! I just backed up ener.edr to ./#ener.edr.1#<BR>> > <BR>> > WARNING: OpenMM does not support leap-frog, will use velocity-verlet <BR>> > integrator.<BR>> > <BR>> > <BR>> > WARNING: OpenMM supports only Andersen thermostat with the <BR>> > md/md-vv/md-vv-avek integrators.<BR>> > <BR>> > <BR>> > WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE <BR>> > and CCMA. Accuracy is based on the SHAKE tolerance set by the <BR>> > "shake_tol" option.<BR>> > <BR>> > <BR>> > WARNING: The OBC scale factors alpha, beta and gamma are hardcoded in <BR>> > OpenMM with the default Gromacs values.<BR>> > <BR>> > <BR>> > Pre-simulation ~15s memtest in progress...done, no errors detected<BR>> > starting mdrun 'Protein'<BR>> > -1 steps, infinite ps.<BR>> > <BR>> > <BR>> > the log file:<BR>> > Input Parameters:<BR>> > integrator = md<BR>> > nsteps = -1<BR>> > init_step = 0<BR>> > ns_type = Grid<BR>> > nstlist = 0<BR>> > ndelta = 2<BR>> > nstcomm = 10<BR>> > comm_mode = Angular<BR>> > nstlog = 0<BR>> > nstxout = 0<BR>> > nstvout = 0<BR>> > nstfout = 0<BR>> > nstcalcenergy = 10<BR>> > nstenergy = 0<BR>> > <BR>> > <BR>> > the nsteps is still -1, did I do something wrong?<BR>> <BR>> You haven't properly commented out the "nsteps = -1" line. The comment sign is <BR>> a ';' not '#' though I'm surprised grompp didn't simply abort with this input file.<BR>> <BR>> -Justin<BR>> <BR>> > <BR>> > Thanks a lot<BR>> > <BR>> > YY<BR>> <BR>> -- <BR>> ========================================<BR>> <BR>> Justin A. Lemkul<BR>> Ph.D. Candidate<BR>> ICTAS Doctoral Scholar<BR>> MILES-IGERT Trainee<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul[at]vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>> <BR>> ========================================<BR>> -- <BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR> </body>
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