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