Hi, i just performed a free energy TI calculation, to get the free energy of solvation of water in water (the chemical potential of water) i stuck closely to the templates given in the tutoral by justin lemkul. The final result i get with g_bar looks good, and the number is within the error-bars of both experiment and literature data - still i keep getting a warning ... i first turn off the charges and then LJ ... but for the LJ part (only) g_bar keeps saying:
WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations. i can't think of anything that's wrong with my simulations, nor do i think this is undersampling (21 windows each 2 nano seconds) also the difference between my mdp and justin's are minor (as i believe, see below) why do i get the correct answer but still this warning keeps coming? at lambda=0 my LJ interactions are fully turned on, and for the DeltaG(0->0.05) i,e, the first row in the table below i get from g_bar: lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0.000 0.050 -2.90 0.03 2.15 0.03 9647088805553410.00 9570465417587940.00 3.30 0.05 0.050 0.100 -3.36 0.03 1.48 0.02 1.47 0.03 1.95 0.02 0.100 0.150 -0.49 0.00 0.03 0.00 0.03 0.00 0.22 0.00 0.150 0.200 0.12 0.00 0.00 0.00 0.00 0.00 0.05 0.00 etc... there appears to be a problem with the phase space overlap, but then all other values, and the end-result, look ok ... can it be that there is an issue with the gmx implementations of soft core potentials and g_bar? cheers mic mdp: ; integrator = sd nsteps = 1000000 ;dt = 0.002 pbc = xyz nstcomm = 100 comm_grps = System ; nstxtcout = 0 nstenergy = 100 nst_log = 100 nstxout = 0 nstvout = 0 ; rlist = 1.0 ; coulombtype = PME rcoulomb = 1.0 vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; DispCorr = EnerPres ; fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; tc_grps = system tau_t = 1.0 ref_t = 300 ; Pcoupl = Berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 pcoupltype = isotropic ; constraints = hbonds lincs_iter = 8 ; free_energy = yes init_lambda = 0.00 delta_lambda = 0.0 foreign_lambda = 0.05 0.10 dhdl_derivatives = yes sc_alpha = 0.5 sc_power = 1 sc_sigma = 0.5 ; i also tried 0.3 same problem nstdhdl = 100 couple-moltype = w1 couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no =============================== Why be happy when you could be normal? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
