I have not really followed the previous email exchange but from this mdp file I wonder what you are trying to achieve. You seem to want to decouple all atoms of your HEPT molecule (couple-moltype, couple-intramol) from its environment but then you also change the masses. What is the physical meaning of a non-interacting final state that has different masses from the initial state? I believe the mass contributions are supposed to cancel in a closed thermodynamic cycle but what is the cycle you are simulating?
On Tue, 16 May 2017 09:30:08 -0400 Dan Gil <dan.gil9...@gmail.com> wrote: > Sorry, here is the mdp file: > > ;Integration Method and Parameters > integrator = sd > nsteps = 100000 > dt = 0.002 > nstenergy = 1000 > nstlog = 5000 > > ;Output Control > nstxout = 0 > nstvout = 0 > > ;Cutoff Schemes > cutoff-scheme = group > rlist = 1.0 > vdw-type = cut-off > rvdw = 2.0 > > ;Coulomb interactions > coulombtype = pme > rcoulomb = 1.0 > fourierspacing = 0.4 > > ;Constraints > constraints = all-bonds > > ;Temperature coupling > tcoupl = v-rescale > tc-grps = system > tau-t = 0.1 > ref-t = 300 > > ;Pressure coupling > pcoupl = parrinello-rahman > ref-p = 1.01325 > compressibility = 4.5e-5 > tau-p = 5 > > ;Free energy calculation > free-energy = yes > init-lambda-state = 8 > delta-lambda = 0 > fep-lambdas = > calc-lambda-neighbors = 1 > vdw_lambdas = 0 0 0 0 0 0 0 0 0 0 0 > coul_lambdas = 0 0 0 0 0 0 0 0 0 0 0 > bonded_lambdas = 0 0 0 0 0 0 0 0 0 0 0 > restraint_lambdas = 0 0 0 0 0 0 0 0 0 0 0 > mass_lambdas = 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 > couple-moltype = HEPT > couple-lambda0 = vdwq > couple-lambda1 = none > couple-intramol = no > nstdhdl = 10 > > > On Tue, May 16, 2017 at 1:02 AM, Mark Abraham > <mark.j.abra...@gmail.com> wrote: > > > Hi, > > > > What use are you making of constraints? Justin suggested sharing a > > full mdp file, which I think may help. We discovered last year that > > you can get equipartition failure for (IIRC) all-bonds constraints > > for moieties like -CH2Cl, and latest grompp now detects this. > > > > Mark > > > > On Tue, 16 May 2017 01:16 Dan Gil <dan.gil9...@gmail.com> wrote: > > > > > Hello, > > > > > > The last thread was getting too big, and the conversation evolved > > > to a topic different from my original question, so I decided to > > > start a new thread. > > > > > > We were discussing thermodynamic integration, and why the > > > mass_lambdas would have any contribution to the derivative of the > > > Hamiltonian. > > > > > > I found a source (link below) which derives the Gibbs free energy > > > change > > as > > > a function of lambda. I learned that the mass contribution is > > > often > > assumed > > > to be small and negligible, given that the mass difference > > > between the > > two > > > lambda states are small. > > > http://www.tandfonline.com/doi/abs/10.1080/00268970600893060 > > > > > > I think that the mass of the two lambda states that equation (14) > > > is referring to is the total mass (mass of solvent plus solute). > > > My system > > is > > > 1 solute (~40 atoms) infinitely diluted in solvent (23500). I > > > wonder if I am getting nonzero mass contributions (in my dhdl.xvg > > > output) because of finite-size effects? Would completely > > > neglecting the mass contributions > > be > > > acceptable? Does doing this technically change the system to one > > > that is > > 1 > > > solute and an infinite number of solvent molecules where the mass > > > contributions limit is zero? > > > > > > Best Regards, > > > > > > Dan > > > -- > > > 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.