Dear Gromacs users I am doing free energy calculation of a ligand with protein. When I do gmx bar it gives me the following error:-
Temperature: 298.15 K Detailed results in kT (see help for explanation): lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0 1 3.29 0.06 1.28 0.10 1.37 0.08 1.54 0.09 1 2 1.41 0.04 0.47 0.05 0.31 0.05 0.77 0.03 2 3 0.88 0.06 0.09 0.02 0.06 0.01 0.41 0.06 3 4 0.67 0.03 -0.01 0.03 -0.01 0.03 0.25 0.01 4 5 0.50 0.01 0.11 0.00 0.10 0.00 0.22 0.01 5 6 0.33 0.01 -0.04 0.01 -0.07 0.03 0.21 0.03 6 7 0.27 0.02 0.07 0.04 0.04 0.02 0.22 0.03 7 8 0.11 0.03 0.05 0.02 0.04 0.01 0.16 0.01 8 9 0.11 0.01 -0.09 0.02 -0.10 0.02 0.17 0.01 9 10 0.08 0.02 0.12 0.01 0.12 0.01 0.20 0.00 10 11 -0.04 0.03 -0.01 0.03 -0.01 0.03 0.18 0.01 11 12 -0.09 0.03 0.06 0.03 0.05 0.03 0.19 0.02 12 13 -0.02 0.03 -0.12 0.03 -0.12 0.03 0.23 0.01 13 14 -0.01 0.03 0.17 0.03 0.16 0.03 0.28 0.02 14 15 -0.06 0.03 -0.09 0.03 -0.09 0.03 0.25 0.01 15 16 -0.04 0.03 0.13 0.04 0.13 0.04 0.29 0.01 16 17 -0.15 0.03 0.04 0.01 0.04 0.01 0.24 0.01 17 18 -0.14 0.03 0.01 0.02 0.01 0.02 0.25 0.01 18 19 -0.07 0.03 -0.01 0.01 -0.08 0.02 0.27 0.01 19 20 -0.05 0.01 0.18 0.00 0.09 0.00 0.28 0.00 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: point 0 - 1, DG 8.14 +/- 0.14 point 1 - 2, DG 3.50 +/- 0.09 point 2 - 3, DG 2.19 +/- 0.14 point 3 - 4, DG 1.66 +/- 0.07 point 4 - 5, DG 1.24 +/- 0.02 point 5 - 6, DG 0.83 +/- 0.02 point 6 - 7, DG 0.66 +/- 0.06 point 7 - 8, DG 0.28 +/- 0.08 point 8 - 9, DG 0.28 +/- 0.03 point 9 - 10, DG 0.19 +/- 0.05 point 10 - 11, DG -0.10 +/- 0.08 point 11 - 12, DG -0.22 +/- 0.07 point 12 - 13, DG -0.05 +/- 0.08 point 13 - 14, DG -0.03 +/- 0.08 point 14 - 15, DG -0.16 +/- 0.07 point 15 - 16, DG -0.10 +/- 0.07 point 16 - 17, DG -0.37 +/- 0.07 point 17 - 18, DG -0.35 +/- 0.08 point 18 - 19, DG -0.17 +/- 0.06 point 19 - 20, DG -0.13 +/- 0.02 total 0 - 20, DG 17.29 +/- 0.47 I have read in the link that I should not have negative entropy values in my simulation https://www.mail-archive.com/gmx-users@gromacs.org/msg55772.html. Can anyone please suggest me what could be wrong during my simulation and how should I fix it? Thank you Sadaf Rani Ph.D. visiting student Lancaster University Uk -- 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.