OK! I got it. I have to put: couple-intramol = yes
but I have to define couple-lambda 0 and couple-lamba-1? how do I turn off the 1-4 pair interaction? 2015-07-17 13:32 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 7/17/15 6:34 AM, Daniele Veclani 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. >> >> > "couple-intramol = no" does not subject intramolecular interactions to > lambda coupling. But doing this in vacuo is pointless, because then by > definition, nothing changes. > > -Justin > > > >> 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? 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > 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.