Dear gmx-usersI want to calculate free energy of binding of ligand to Au surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file: title = n.pdb restraining cpp = /lib/cpp constraints = all-bonds constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 integrator = sd dt = 0.0008 nsteps = 2500000 nstcomm = 100 nstcalcenergy = 100 nstdhdl = 100 comm_mode = nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.4 ;rlistlong = 2 coulombtype = PME rcoulomb = 1.4 rcoulomb-switch = 0.8 rvdw = 1 vdwtype = shift rvdw-switch = 0.9 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 = Parrinello-Rahman Pcoupltype = isotropic tau_p = 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 freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y free-energy = yes couple-moltype = Protein2 init-lambda = 0 sc-power = 1 sc-sigma = 0.3 sc-alpha = 1 couple-intramol = no couple-lambda1 = vdwq couple-lambda0 = none foreign-lambda = &ALL_LAMBDAS$ As you can see dt= 0.0008, for 8 ns simulation, I should take the nstep of each Lambda 10000 ( or I should divide 8 ns between 7 Lambda)? In other words, the simulation time for each of the 7 lambda should be 8 ns or every lambda simulation time should be considered so that the total simulation time of lambdas be 8 ns? I hope I could correctly ask my question. I would greatly appreciate your response to my question. Fatemeh Ramezani -- Gromacs Users mailing list
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