Dear, is there a tutorial to run Hamiltonian replica exchange in gromacs?? and could you please see if the mdp setting is right to run Hamiltonian replica exchange of lipid system using a coarse-grained method?
integrator = sd tinit = 0.0 dt = 0.030 nsteps = 15000000 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstxout-compressed = 5000 compressed-x-precision = 100 cutoff-scheme = Verlet nstlist = 20 ns_type = grid pbc = xyz verlet-buffer-tolerance = 0.005 epsilon_r = 15 coulombtype = reaction-field rcoulomb = 1.1 vdw_type = cutoff vdw-modifier = Potential-shift-verlet rvdw = 1.1 tc-grps = membrane solute tau_t = 1.0 1.0 ref_t = 323 323 ; Pressure coupling: Pcoupl = Parrinello-rahman Pcoupltype = isotropic tau_p = 12.0 compressibility = 4.5e-5 ref_p = 1.0 ; Free energy control stuff free_energy = no init_lambda_state = 0 delta_lambda = 0 calc_lambda_neighbors = 1 ; only immediate neighboring windows ; Vectors of lambda specified here ; Each combination is an index that is retrieved from init_lambda_state for each simulation ; init_lambda_state 0 1 2 3 4 5 6 7 8 9 10 11 coul-lambdas = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 vdw-lambdas = 1.00 0.95 0.90 0.85 0.80 0.75 0.70 0.65 0.60 0.55 0.50 0.45 bonded-lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint-lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Not doing simulated temperting here temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = yes ; linear interpolation of Coulomb (none in this case) sc-power = 1 sc-sigma = 0.3 couple-moltype = CHOL ; name of moleculetype to decouple couple-lambda0 = vdw-q ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = none ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix refcoord_scaling = all Regards, Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.