Dear Gmx Users, I obtained a protein-ligand complex from 100ns simulation. Now I am pulling my ligand away from the protein after the energy minimzation in water and equilibration of 100ps (two coupling baths: Protein, LIG_Water_and_ions). Then I proceed my pulling :
grompp -f pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr mdrun -s pull.tpr -deffnm pull title = Umbrella pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 500000 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 0 nstvout = 0 nstfout = 500 nstxtcout = 1000 ; 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 = 1.2 vdwtype = Switch rvdw-switch = 1.0 ; 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 ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc_grps = Protein LIG_Water_and_ions ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 298 298 ; reference temperature, one for each group, in K ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 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 ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = LIG pull_rate1 = 0.004 ; 0.004 nm per ps = 4 nm per ns pull_k1 = 500 ; kJ mol^-1 nm^-2 I run 3 pulling simulations with the same mdp and I obtain 3 different profiles (Force vs time). Then I used 2xlonger pulling with the same pulling distance and I run 3 simulations again. Each time I obtain different profile. Can anyone explain me this? I am using velocities from npt simulation as above (gen_vel = no and continuation = yes) so I presume the output should be similar. Please, advice. Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists