Dear Justin and Gmx Users,<br><br>I run a pulling of my ligand away from
my protein with the same mdp file and I obtained two different plots -
Force vs time (The breaking point occured at different times with different force). Can you please explain?<br>
My mdp file:<br><br>title = Umbrella pulling simulation <br>define = -DPOSRES_L<br>; Run parameters<br>integrator = md<br>dt = 0.002<br>tinit = 0<br>nsteps = 250000 ; 0.5ns<br>nstcomm = 10<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 = 0.9<br>rcoulomb = 0.9<br>rvdw = 0.9<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>
; Temperature coupling is on<br>tcoupl = V-rescale ; modified Berendsen thermostat<br>tc_grps = Protein_LIG Water_and_ions ; two coupling groups - more accurate<br>tau_t = 0.1 0.1 ; time constant, in ps<br>
ref_t = 298 298 ; reference temperature, one for each group, in K<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 ; simple distance increase <br>pull_dim = N N Y<br>pull_start = yes ; define initial COM distance > 0<br>pull_ngroups = 1<br>
pull_group0 = Protein <br>pull_group1 = LIG182 <br>pull_rate1 = 0.016 ; 0.008 nm per ps = 8 nm per ns<br>pull_k1 = 200 ; kJ mol^-1 nm^-2