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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