[gmx-users] ./mdrun

[lin hen]

yeah，Thanks a lot :)
 
YY
 
 
> Date: Thu, 11 Nov 2010 20:32:55 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] ./mdrun
> 
> 
> 
> lin hen wrote:
> > It doesn't work, even I deleted this line....
> > it stills shows the same error...
> > 
> 
> Did you re-generate the .tpr file? I see no reason that a suitable setting for 
> nsteps would be magically substituted by either grompp or mdrun.
> 
> > I use ./mdrun-gpu without any flags. Did I miss something?
> > 
> 
> Is the correct .tpr file being read in? Without any flags, mdrun will look for 
> "topol.tpr" by default. If this is not the file you've created, then you're 
> just re-running the same malformed input.
> 
> -Justin
> 
> > YY 
> > > Date: Thu, 11 Nov 2010 20:25:45 -0500
> > > From: jalemkul at vt.edu
> > > To: gmx-users at 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
> > >
> > > ========================================
> > > --
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> 
> -- 
> ========================================
> 
> 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
> 
> ========================================
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