I do not know how your top file looks like and what you have done to it. The setup procedure to create the topolog file would be as for a standard MD simulation with M. You would make sure that the "QUI" label referes to the right indexes in your index file and run TI with you preferred protocol. This simplified setup procedure ensures that you do not have to modify the topology file in any way esp. not to have to set up an explicit B state.
I suggest to read all parts relating to couple-* in the manual. This is scattered over several places in the text. Cheers, Hannes. ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Daniele Veclani [danielevecl...@gmail.com] Sent: 17 July 2015 08:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] solvation free energy Thank you for your answer. I read the manual. As I understand it, I should be deleted, from .top file, the section of non-bonded parameters. It's right? Of course, after the VdW I'll change the electrostatic transformation. Best regards D.V. 2015-07-16 16:55 GMT+02:00 Hannes Loeffler <hannes.loeff...@stfc.ac.uk>: > 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. > -- 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. -- 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.
