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

[sitiazma]

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

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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