Cheers Chris Is the best way to check for convergence; to keep adding in more histograms until the curves converge. Also your comment 'don't remove any data', do you mean to keep histograms that are not so good.
Gavin chris.ne...@utoronto.ca wrote: > your comment: > > which should be centred around 0.80nm > > is flawed, as i mentioned earlier. also, it is not g_wham that is > sensitive but the convergence and sampling of phase space that is > sensitive. don`t remove any data. do evaluate your convergence. > without convergence measures, a pmf is worse than useless. > > chris. > > -- original message -- > > Cheers Chris > > If I remove the red histogram (the first of the wider distributions), > which should be centred around 0.80nm but is actually centred around > 0.78 nm; and add in some more histograms with higher force constants the > profile changes slightly. It seems that g_wham is very sensitive to > these subtleties. How do I know which curve is correct? I have about six > such curves that differ slightly in this manner. > > Gavin > > chris.ne...@utoronto.ca wrote: > > [Hide Quoted Text] > looks fine to me, no need to do that extra sampling that I suggested > since it appears that you already did this -- benefits of seeing real > data ;). If you want to understand why your histograms are not always > centered at r0 (note that this is just fine) then you should read more > about US, WHAM, and how to bias/debias the data for US (I am sure that > there are textbooks around that explain this). The only case in which > all of your histograms will be centered at their respective r0 is when > the underlying PMF is exactly flat. > > Chris. > > -- original message -- > > Hi Chris many thanks again for the advise. I have, or at least I thought > have sampled my barrier region to death, but as I say some histograms > may not be centred around r0. I will proceed with what you suggest. > Please find attached a picture of the histograms, the corresponding > profile, and a sample mdp file that I use. > > -- 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
