On 4/26/15 8:54 AM, fatemeh ramezani wrote:
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?
How have you predetermined that you want 8 ns total, split over 7 states? You should do some test runs to assess convergence and determine how much sampling per state is necessary, rather than just assume a certain time.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
