Dear Justin I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for water.
em.mdp file: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 40000 constraint_algorithm = shake_tol = 0.0001 nstenergy = 10 nstxtcout = 1 nstlist = 5 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 8 ewald_rtol = 1e-5 optimize_fft = yes emtol = 1000.0 emstep = 0.01 md.mdp file: title = n.pdb restraining cpp = /lib/cpp constraints = none integrator = md dt = 0.0008 nsteps = 25000000 nstcomm = 10 comm_mode = nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rcoulomb-switch = 1 rvdw = 0.5 vdwtype = shift ;rvdw-switch = 0.6 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in three groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Protein Non-Protein ref_t = 300 300 ; Pressure coupling is on ;Pcoupl = berendsen Pcoupl = no Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 energygrps = Protein Sol Fatemeh Ramezani -- 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