[gmx-users] ./mdrun

[Justin A. Lemkul]

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

-- 
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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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