[gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file

[Justin A. Lemkul]

sitiazma wrote:
> Hi gromacs users,
> 
> does anyone knows why I got this error
> from grompp
> 
>  > grompp -f run.mdp -o dmpc.tpr -c dmpc.pdb -n index.ndx -p topol.top
> 
> WARNING 1 [file run.mdp, line unknown]:
>   Unknown left-hand iconstraint_algorithm in parameter file
> 

You have a typo.  The error message is pretty explicit that you've typed 
something wrong.

-Justin

> I run gromacs 3.1.4 to make a hole in lipids using MSMS
> below is my run.mdp
> 
> title               =  Make Hole for myprotein
> ;define              =  -DPOSRES
> constraints              = all-bonds
> iconstraint_algorithm     = Lincs
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  5000000  ; total 1 ns.
> 
> ; remove center of mass translation and rotation around center of mass
> comm_mode           =  Linear
> nstcomm             =  1
> comm-grps           =
> ;nstxout            =  500
> ;nstvout            =  10000
> ;nstfout            =  0
> ;nstlog             =  10
> ;nstenergy          =  10
> 
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout                  = 10000
> nstvout                  = 10000
> nstfout                  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog                   = 500
> nstenergy                = 500
> ; Output frequency and precision for xtc file =
> nstxtcout                = 100
> xtc_precision            = 1000
> ; This selects the subset of atoms for the xtc file. You can =
> ; select multiple groups. By default all atoms will be written. =
> xtc-grps                 =
> ; Selection of energy groups =
> energygrps               =
> 
> 
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist                  = 10
> ; ns algorithm (simple or grid) =
> ns_type                  = grid
> ; Periodic boundary conditions: xyz or no =
> pbc                      = xyz
> ; nblist cut-off         =
> rlist                    = 1
> domain-decomposition     = no
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW =
> ; Method for doing electrostatics =
> coulombtype              = PME
> rcoulomb_switch          = 0
> rcoulomb                 = 1.0
> ; Dielectric constant (DC) for cut-off or DC of reaction field =
> epsilon_r                = 1
> ; Method for doing Van der Waals =
> vdw-type                 = Cut-off
> ; cut-off lengths        =
> rvdw_switch              = 0
> rvdw                     = 1.0
> ; Apply long range dispersion corrections for Energy and Pressure =
> DispCorr                 = No
> ; Spacing for the PME/PPPM FFT grid =
> fourierspacing           = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used =
> fourier_nx               = 0
> fourier_ny               = 0
> fourier_nz               = 0
> ; EWALD/PME/PPPM parameters =
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = yes
> 
> ; Temperature coupling   =
> Tcoupl                   = Berendsen
> ; Groups to couple separately =
> tc_grps                  = DMP SOL
> ; Time constant (ps) and reference temperature (K) =
> tau_t                    = 0.1 0.1
> ref_t                    = 310 310
> ; Pressure coupling      =
> Pcoupl                   = Berendsen
> Pcoupltype               = semiisotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p                    = 1.0 1.0
> compressibility          = 4.5e-5 4.5e-5
> ref_p                    = 1.0 1.0
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel                  = yes
> gen_temp                 = 310
> gen_seed                 = 512329
> 
> Thanks a lot.
> Siti
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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