[gmx-users] ./mdrun

[lin hen]

It doesn't work, even I deleted this line....
it stills shows the same error...
 
I use ./mdrun-gpu without any flags. Did I miss something?
 
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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