Michael, Thank you so much for such a quick and detailed response. I tried to increase the number of intermediate lambda windows, but unfortunately, it was not possible to reduce the error to an acceptable level.
coul-lambdas = 0.0 0.02 0.05 0.08 0.12 0.16 0.2 0.3 0.4 0.6 0.7 0.8 0.84 0.88 0.92 0.95 0.98 1.0 point 0 - 1, DG 47.68 +/- 0.13 point 1 - 2, DG 34.31 +/- 0.56 point 2 - 3, DG 19.42 +/- 0.97 point 3 - 4, DG 15.56 +/- 1.07 point 4 - 5, DG 8.45 +/- 0.03 point 5 - 6, DG 3.53 +/- 0.02 point 6 - 7, DG 4.99 +/- 0.02 point 7 - 8, DG 2.30 +/- 0.02 point 8 - 9, DG -0.02 +/- 0.03 point 9 - 10, DG -2.79 +/- 0.31 point 10 - 11, DG -5.74 +/- 0.72 point 11 - 12, DG -6.58 +/- 0.45 point 12 - 13, DG -8.02 +/- 0.03 point 13 - 14, DG -8.60 +/- 0.03 point 14 - 15, DG -15.92 +/- 0.04 point 15 - 16, DG -33.08 +/- 1.38 point 16 - 17, DG -47.34 +/- 1.22 total 0 - 17, DG 8.15 +/- 1.69 As for the three-level transformation, I agree that it should help, but it seems I don’t quite understand how to implement this behavior in GROMACS. I don't know by which options of the .mdp file it should be implemented and how to build topology files for such transformations. If you provided me with a small example of an mdp and itp file for such a transformation, I would be very grateful to you. Thank you, Shekhovtsov Artem On Wed, Jan 23, 2019 at 7:00 PM Michael Shirts <mrshi...@gmail.com> wrote: > As free energies get larger, then the error gets less accurate. So if it is > reporting 18.51 +/- 2.95 for one of the intervals, that likely suggest > there is very little overlap in that area. > A total free energy difference of in -6.12 +/- 3.19 for the > transformation indicates that the result is not very certain; you're within > two standard deviations, and again, the Bennett error formula is inaccurate > for larger error. I would suggest adding 1-2 more intermediates between > those points. > > https://github.com/MobleyLab/alchemical-analysis provides some of the > tools > to check overlap. > > I would also suggest doing a multi stage transformation to increase overlap > - for atoms that are disappearing or appearing that are charged, turn off > charges off, change vdw, then turn charges back on. In some cases, > especially when the atoms involved have different sizes, sc-coul can lead > to some semi-pathological cases when vdw softcore and coul softcore result > in some very low/high potentials at intermediates. > > On Wed, Jan 23, 2019 at 8:21 AM Artem Shekhovtsov < > job.shekhovt...@gmail.com> > wrote: > > > Hi all! > > I encountered an error in my relative free energy calculations and do not > > know how to fix it. > > Molecules for which I want to carry out calculations contain a carboxyl > > group. > > To validate the protocol, I tried to run the fep-calculations of > symmetric > > molecules for which the change in free energy will be zero. > > During validation, I was faced with the fact that the convergence error > for > > charged ligands greatly exceeds that for neutral ones. > > For example, for the case of m-methyl benzoic acid [O-]C(= O)c1cc(C)ccc1: > > Mutation (-CH3 + H) for one meta position (-H + CH3) for another meta > > position relative to the carboxyl group. > > > > Ionized acid (solvent leg, 5 ns): > > point 0 - 1, DG 28.74 +/- 0.02 > > point 1 - 2, DG 53.79 +/- 0.41 > > point 2 - 3, DG 27.76 +/- 2.45 > > point 3 - 4, DG 18.51 +/- 2.95 > > point 4 - 5, DG 8.80 +/- 0.79 > > point 5 - 6, DG 4.04 +/- 0.07 > > point 6 - 7, DG -0.06 +/- 0.04 > > point 7 - 8, DG -2.62 +/- 0.33 > > point 8 - 9, DG -8.95 +/- 0.27 > > point 9 - 10, DG -23.89 +/- 1.61 > > point 10 - 11, DG -29.32 +/- 1.29 > > point 11 - 12, DG -54.15 +/- 0.08 > > point 12 - 13, DG -28.79 +/- 0.03 > > > > total 0 - 13, DG -6.12 +/- 3.19 > > > > Unionized acid (solvent leg, 5 ns): > > point 0 - 1, DG 0.08 +/- 0.01 > > point 1 - 2, DG -6.88 +/- 0.10 > > point 2 - 3, DG -14.69 +/- 0.05 > > point 3 - 4, DG -21.07 +/- 0.03 > > point 4 - 5, DG -13.21 +/- 0.02 > > point 5 - 6, DG -7.46 +/- 0.02 > > point 6 - 7, DG -0.09 +/- 0.03 > > point 7 - 8, DG 7.37 +/- 0.02 > > point 8 - 9, DG 13.24 +/- 0.03 > > point 9 - 10, DG 21.15 +/- 0.06 > > point 10 - 11, DG 14.72 +/- 0.03 > > point 11 - 12, DG 6.98 +/- 0.07 > > point 12 - 13, DG -0.05 +/- 0.01 > > > > total 0 - 13, DG 0.09 +/- 0.22 > > > > For a neutral molecule containing a charged carboxyl and amino groups > > ([O-]C(=O)c1cc(C)c([NH3+])cc1) the error is small: > > point 0 - 1, DG -4.65 +/- 0.01 > > point 1 - 2, DG -19.95 +/- 0.04 > > point 2 - 3, DG -28.67 +/- 0.13 > > point 3 - 4, DG -57.84 +/- 0.19 > > point 4 - 5, DG -44.18 +/- 0.08 > > point 5 - 6, DG -26.84 +/- 0.05 > > point 6 - 7, DG 0.10 +/- 0.20 > > point 7 - 8, DG 26.92 +/- 0.06 > > point 8 - 9, DG 44.28 +/- 0.13 > > point 9 - 10, DG 57.79 +/- 0.13 > > point 10 - 11, DG 28.68 +/- 0.09 > > point 11 - 12, DG 19.98 +/- 0.12 > > point 12 - 13, DG 4.66 +/- 0.03 > > > > total 0 - 13, DG 0.28 +/- 0.21 > > > > Adding Na and Cl ions to ([O-]C(=O)c1cc(C)c([NH3+])cc1) does not cause an > > increase in error. > > point 0 - 1, DG -4.61 +/- 0.01 > > point 1 - 2, DG -19.96 +/- 0.07 > > point 2 - 3, DG -28.68 +/- 0.04 > > point 3 - 4, DG -57.67 +/- 0.04 > > point 4 - 5, DG -44.24 +/- 0.01 > > point 5 - 6, DG -26.91 +/- 0.04 > > point 6 - 7, DG 0.03 +/- 0.03 > > point 7 - 8, DG 26.89 +/- 0.03 > > point 8 - 9, DG 44.20 +/- 0.08 > > point 9 - 10, DG 57.75 +/- 0.09 > > point 10 - 11, DG 28.65 +/- 0.06 > > point 11 - 12, DG 20.02 +/- 0.05 > > point 12 - 13, DG 4.67 +/- 0.01 > > > > total 0 - 13, DG 0.12 +/- 0.18 > > > > FEP-part of *.mdp: > > free-energy = yes > > sc-power = 1 > > sc-alpha = 0.5 > > sc-coul = yes > > fep-lambdas = 0.0 0.01 0.05 0.1 0.2 0.3 0.4 0.6 > 0.7 > > 0.8 0.9 0.95 0.99 1.0 > > coul-lambdas = 0.0 0.01 0.05 0.1 0.2 0.3 0.4 0.6 > 0.7 > > 0.8 0.9 0.95 0.99 1.0 > > vdw-lambdas = 0.0 0.01 0.05 0.1 0.2 0.3 0.4 0.6 > 0.7 > > 0.8 0.9 0.95 0.99 1.0 > > > > What is the reason of such error and how I can fix it? > > > > mdp, itp, gro, xvg files by link - > > https://drive.google.com/open?id=1MiepOQb2QAZ9rclpY13owCnl8QWcTHnf > > Ready to provide any additional information. > > > > Thank you, > > Shekhovtsov Artem > > -- > > 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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