Hi Mark, Thanks for the catch on the transcription error, I think I have found it ::embarrassed::. The repeated final value is still perplexing me. I have checked both my .xvg from g_energy and the .edr file with gmxdump. In both cases the final step (time value) only occurs once, and the second last time point has different values. This is a single run so I don't think I should have concatenation issues?
I just checked the counts and there are 476 time points in the energy file and 477 in the g_lie file. All the best, Tom On 14/06/2012 3:56 PM, Tom Dupree wrote: > Greetings all, > I can't manually reproduce g_lie results. > After raging at excel for a while I think I have found a bug. > > Here is my first time point, > Reported by g_lie to be 35.0073 > > From energy file > Lj_complex =-130.762 > Coul_complex = -286.746 > My constants specified to g_lie > Clj = Alpha = lj_const = 0.181 > Cqq = Beta = coul_const = 0.43 > Elj = Lj_solv = -166 > Eqq = Coul_solv = -263 > > Therefore > Lj_diff = 35.238 > Coul_diff = -23.746 > > Hence > Lj_diff x lj_const = 6.378 > Coul_diff x coul_const = -10.211 > > And there is no way I can add those to get 35.0073 > > However I can get this value using the following > Coul_complex - lj_solv = -120.746 > Lj_complex - coul_solv = 132.2378 > -120.746 x lj_const = -120.746 x 0.181 = -21.855 > 132.2378 x coul_const = 56.86225 > Sum = 35.00726 > > In short I think the g_lie calculation has swapped its variables, Elj instead > of Eqq and vice versa. I think it's rather more likely you've made a transcription error going to Excel. You can check the code of src/tools/gmx_lie.c for exactly this kind of purpose, but I can't see any problem with it. > > One other thing I have noticed is that when calculating the average g_lie > uses the final value twice, is there a reason for this? > > e.g. > > 994 24.9397 > 996 43.3382 > 998 40.5714 > 1000 40.5585 > 1000 40.5585 > Inspect your energy file with gmxdump - I think you've managed to duplicate the final frame at an earlier point of your workflow. eneconv has options to prevent such duplicates occuring during concatenation, etc. In any case, g_lie just eats what you give it... Mark -- 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
