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
