[gmx-users] make hole with gromacs 3.1.4 error : Unknown left-hand iconstraint_algorithm in parameter file
sitiazma
sitiazma at gmail.com
Fri Mar 13 15:50:42 CET 2009
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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