The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional "correction" in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation.
On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani <danielevecl...@gmail.com> wrote: > 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.
