1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 40000 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein SOL freezedim = Y Y Y Y Y Y comm_mode = None
2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 40000 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None 3. In simulation, I'm using this md.mdp file: title = Yo cpp = /lib/cpp define = integrator = md tinit = 0.00000 dt = 0.002 nsteps = 250000 nstxout = 2500 nstvout = 2500 nstlog = 500 nstenergy = 250 nstxtcout = 0 pbc = xyz rlist = 1.00 coulombtype = PME r_coulomb = 1.00 fourierspacing = 0.10 pme_order = 6 ewald_rtol = 1e-6 vdw-type = switch rvdw-switch = 0.90 rvdw = 1.00 tcoupl = nose-hoover tc_grps = SOL AUS AUB AUI tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 Pcoupl = no gen_vel = yes gen_temp = 10 gen_seed = 173529 ; GolP has been tested with lincs only constraints = none constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 lincs_warnangle = 80 freezegrps = AU AUI freezedim = Y Y Y Y Y Y comm_mode = None Are these .mdp file right? 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
