I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water ---> dum+water
Now I have to do: M(vacuo) --> dum(vacuo) In this case I have a problem, in fact I find a DG = 0.00000 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit = 0 dt = 0.002 nsteps = 2500000 comm_mode = angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy = 500 nstxout-compressed = 0 cutoff-scheme = group nstlist = 0 ns_type = simple pbc = no rlist = 0 coulombtype = cutoff rcoulomb = 0 epsilon_r = 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t = 0.1 ref_t = 300 Pcoupl = no tau_p = 1.0 compressibility = 4.5e-05 ref_p = 1.0 free_energy = yes init_lambda_state = 0 delta_lambda = 0 calc_lambda_neighbors = 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 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 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 Best regards Daniele Veclani. -- 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.