Hi, I am trying to compute the free energy change using g_bar: I am using two-stage decoupling process as in Justin Lemkul's tutorial. But , I get following warning in all cases regarding violation of second law of thermodynamics. Can someone explain what is this error about and which lambda I should look for? Here is the output.
Detailed results in kT (see help for explanation): lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0.000 0.100 -0.39 0.08 -0.64 0.06 -0.09 0.20 0.88 0.05 0.100 0.150 0.08 0.04 0.07 0.03 0.09 0.05 0.43 0.01 0.150 0.200 0.12 0.02 -0.11 0.03 0.36 0.06 0.54 0.02 0.200 0.300 0.54 0.06 -0.05 0.07 1.25 0.15 1.24 0.03 0.300 0.350 0.21 0.03 0.15 0.04 0.31 0.06 0.72 0.01 0.350 0.400 -0.01 0.02 0.11 0.03 -0.08 0.04 0.64 0.01 0.400 0.500 -0.37 0.03 0.22 0.02 -0.78 0.06 1.07 0.01 0.500 0.600 -0.58 0.01 0.17 0.04 -1.17 0.04 0.99 0.01 0.600 0.700 -0.74 0.03 0.16 0.02 -1.51 0.07 0.89 0.01 0.700 0.750 -0.37 0.01 -0.02 0.02 -0.69 0.03 0.47 0.01 0.750 0.800 -0.26 0.01 -0.07 0.01 -0.42 0.02 0.53 0.01 0.800 0.850 -0.19 0.01 0.03 0.01 -0.38 0.03 0.57 0.01 0.850 0.900 -0.24 0.02 0.06 0.01 -0.50 0.04 0.58 0.01 0.900 1.000 -0.47 0.07 -0.04 0.05 -0.12 0.34 1.13 0.06 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. Final results in kJ/mol: lambda 0.000 - 0.100, DG -0.97 +/- 0.19 lambda 0.100 - 0.150, DG 0.20 +/- 0.09 lambda 0.150 - 0.200, DG 0.30 +/- 0.05 lambda 0.200 - 0.300, DG 1.34 +/- 0.15 lambda 0.300 - 0.350, DG 0.52 +/- 0.07 lambda 0.350 - 0.400, DG -0.02 +/- 0.05 lambda 0.400 - 0.500, DG -0.92 +/- 0.08 lambda 0.500 - 0.600, DG -1.45 +/- 0.03 lambda 0.600 - 0.700, DG -1.86 +/- 0.08 lambda 0.700 - 0.750, DG -0.91 +/- 0.03 lambda 0.750 - 0.800, DG -0.64 +/- 0.03 lambda 0.800 - 0.850, DG -0.48 +/- 0.03 lambda 0.850 - 0.900, DG -0.61 +/- 0.04 lambda 0.900 - 1.000, DG -1.17 +/- 0.18 total 0.000 - 1.000, DG -6.68 +/- 0.30 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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