Dear All I am using this configuration.mdp file for pulling.this is the same as umbrella sampling,of course I have changed some parts of it according to my problem(protein-ligand free energy).but when i use grompp this warning is occuring. WARNING 1 [file configuration.mdp, line unknown]: Unknown left-hand 'continuation' in parameter file
WARNING 2 [file configuration.mdp, line unknown]: Unknown left-hand 'pull' in parameter file WARNING 3 [file configuration.mdp, line unknown]: Unknown left-hand 'pull_geometry' in parameter file WARNING 4 [file configuration.mdp, line unknown]: Unknown left-hand 'pull_dim' in parameter file WARNING 5 [file configuration.mdp, line unknown]: Unknown left-hand 'pull_start' in parameter file WARNING 6 [file configuration.mdp, line unknown]: Unknown left-hand 'pull_ngroups' in parameter file WARNING 7 [file configuration.mdp, line unknown]: Unknown left-hand 'pull_group0' in parameter file WARNING 8 [file configuration.mdp, line unknown]: Unknown left-hand 'pull_group1' in parameter file WARNING 9 [file configuration.mdp, line unknown]: Unknown left-hand 'pull_rate1' in parameter file WARNING 10 [file configuration.mdp, line unknown]: Unknown left-hand 'pull_k1' in parameter file I copy my .mdp file.where of it is wrong?? title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250000 ; 500 ps nstcomm = 1 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance pull_dim = N Y N pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = protein pull_group1 = LIG pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 thanks in advance Mohsen
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