[gmx-users] ./mdrun

[Justin A. Lemkul]

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

========================================