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: 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
>
> ========================================
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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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