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yeah,Thanks a lot :)<BR>
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YY<BR>
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> Date: Thu, 11 Nov 2010 20:32:55 -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>> > It doesn't work, even I deleted this line....<BR>> > it stills shows the same error...<BR>> > <BR>> <BR>> Did you re-generate the .tpr file? I see no reason that a suitable setting for <BR>> nsteps would be magically substituted by either grompp or mdrun.<BR>> <BR>> > I use ./mdrun-gpu without any flags. Did I miss something?<BR>> > <BR>> <BR>> Is the correct .tpr file being read in? Without any flags, mdrun will look for <BR>> "topol.tpr" by default. If this is not the file you've created, then you're <BR>> just re-running the same malformed input.<BR>> <BR>> -Justin<BR>> <BR>> > YY <BR>> > > Date: Thu, 11 Nov 2010 20:25:45 -0500<BR>> > > From: jalemkul@vt.edu<BR>> > > To: gmx-us
ers@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>> > &
gt; > 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 <BR>> > comment sign is<BR>> > > a ';' not '#' though I'm surprised grompp didn't simply abort with <BR>> > this input file.<BR>> > ><BR>> > > -Justin<BR>> > ><BR>> > > ><BR>> > > > Thanks a lot<BR>> > > ><BR>> > > > YY<BR>> > ><BR>> > > --<BR>> > > ========================================<BR>> > &
gt;<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 <BR>> > 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<B
R>> <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><BR>                                            </body>
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