Hi Deepak, I am battling the same problem too. I am doing free energy calculation for heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1.

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Like Andre said, there is expected to be a free energy change when you change the mass of a particle. But if you do the same transformation from Li+ to Cl- in the gas phase, hopefully the free energy change will be opposite and (approximately) equal. Have you tried doing this second calculation [Li+ -> Cl-] in the gas phase? I think this website: http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this second step might be needed better. Dan On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura <mo...@ufscar.br> wrote: > Deepak, > > I never did a mass perturbation myself, but I would expect some free energy > change, since the translational partition function depends on the mass of > the molecules. > > Also, having the same kinetic energy is not meaningful at all, the correct > quantity you should always use in statistical mechanics reasoning is the > momentum of the particle, p=mv, which clearly changes during your > alchemical transformation. Put in another way: the phase space of the > system is a 6N dimensional space of positions and momenta, and you have > just perturbed the momenta part. > > And by the way: that is a typical case in which Monte Carlo methods would > fail to reproduce an MD result, since only the configurational phase space > is sampled in MC (masses effects would have to be added afterwards, > assuming that some analytical result could be computed) > > I hope it helps > > Andre > > On Fri, Aug 11, 2017 at 6:36 AM, deepak bapat <duba...@gmail.com> wrote: > > > Dear Gmx Users > > > > I am trying to find out free energy of transforming one neutral LI to one > > CL in aqueous solution. > > > > Water model is SPC/E. Gromacs version: 5.1.2 > > > > I am doing something like this > > > > Insert 1 Li olecule in water. (Li parameters were taken from Kasper P. > > Jensen and William L. Jorgensen 2006.) > > > > step 1: increase mass of atom from 6.94100 to 35.45300. > > > > Step 2: change LJ parameters of LI to LJ of CL > > > > > > Now my doubt is in step 1: i get non zero free energy values. > > > > *required nonbonded.itp file content is* > > > > ;LI+ > > opls_406 LI 3 6.94100 0.000 A 2.8700e-01 2.0929e-03 > > ; Li+ parameters from jensen and jorgensen JCTC 2006 2 1499-1509 > > > > ;LI+ grown > > opls_407 LI 17 35.45300 0.000 A 2.8700e-01 2.0929e-03 > > ; Li+ parameters from jensen and jorgensen JCTC 2006 2 1499-1509 ;; Mass > of > > chlorine > > > > > > *LI.itp file content of alchemical transformation for mass is* > > [ atoms ] > > ; id at type res nr residu name at name cg nr charge mass > > 1 opls_406 1 LI LI 1 0.0 6.941 > > opls_407 0.0 35.45300 > > > > > > *.mdp file used is as follows* > > > > > > integrator = sd > > tinit = 0 > > dt = 0.001 > > nsteps = 1000000 > > nstcomm = 100 > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > nstlog = 5000 > > nstenergy = 5000 > > nstxtcout = 500 > > cutoff-scheme = verlet > > nstlist = 10 > > ns_type = grid > > pbc = xyz > > rlist = 1.0 > > coulombtype = PME > > rcoulomb = 1.0 > > vdwtype = cutoff > > rvdw = 1.0 > > DispCorr = EnerPres > > fourierspacing = 0.12 > > pme_order = 6 > > tc_grps = system > > tau_t = 1.0 > > ref_t = 300 > > Pcoupl = Parrinello-Rahman > > tau_p = 1.0 > > compressibility = 4.5e-05 > > ref_p = 1.0 > > free_energy = yes > > init_lambda = 0.05 ;;; depending on state, lambda value to be changed > from > > 0 to 1 ;;;;; > > delta_lambda = 0 > > nstdhdl = 10 > > gen_vel = no > > constraints = h-bonds > > constraint-algorithm = lincs > > continuation = yes > > lincs-order = 12 > > > > > > Free enegy of step 1: i.e. mass transfomation is around +6.2 kJ/mol. > > > > In Gromacs 5.1.2 manual section 4.5 p.no 99 dependance of free energy on > > lambda equation is given. > > > > Now my doubt is if I am using the NPT ensemble then the total kinetic > > energy of the system should be constant i.e. summation(p^2/2m) which is > > being controlled by the thermostat. > > > > But i am getting non zero value in this case? Is it normal to get > something > > like this or i have blundered somewhere? > > > > Will be happy to share input files if it helps. > > > > Thanks and Regards > > > > -- > > Deepak U. Bapat > > -- > > 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. > > > > > > -- > _____________ > > Prof. Dr. André Farias de Moura > Department of Chemistry > Federal University of São Carlos > São Carlos - Brazil > phone: +55-16-3351-8090 > -- > 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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