What happens when you do both transformations simultaneously, i.e. sc-coul=yes?
On Mon, 27 Jul 2015 15:55:04 +0200 Daniele Veclani <danielevecl...@gmail.com> wrote: > I'm trying to calculate the solvation free energy of a molecule (M). > > I have done a VdW. transformation. > > I have done also a electrostatic transformation. But I get an > incorrect value (large overestimation of DG solvation). > > I use gromacs 5.0.4 with gromos 54a7 force fields 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 = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 > 1.00 1.00 1.00 > coul_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 > 0.80 0.90 1.00 > 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-q > > couple-lambda1 = vdw > 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 > > > What's wrong? > > Best regards > D.V. -- 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.