Any particular reason why you want to do it the hard way? I suspect the answer to this is somewhere in section 5.3 where [pairs_nb] is discussed. You would have to explicitly set A and B states and not use couple-*. You may find some old-style input files on http://www.alchemistry.org/wiki/Main_Page .
On Fri, 17 Jul 2015 12:34:42 +0200 Daniele Veclani <danielevecl...@gmail.com> wrote: > I read the manual and also some examples of free energy calculation. > > when I do the simulation: > M(vacuo) --> nothing(vacuo) > > I leave only intramolecular interactions. > > How can I just leave these interactions? I don't find the answer in > the manual. > > > Best regards > D.V. > > 2015-07-17 10:10 GMT+02:00 <hannes.loeff...@stfc.ac.uk>: > > > 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? 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