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