Hi, I have a umbrella sampling simulation where we are pulling fragments of a protein dimer away from each other. While selecting the windows, we have used a 0.1 nm spacing. When I perform a g_wham by using all the windows, I have PMF profile that is not smooth on the left hand side. But when I exclude some of the windows, then I have a more smooth PMF profile on the left hand side, which is more similar to what we want to have. You can find both PMF curves and the histograms below.
PMF curve with all windows: https://drive.google.com/file/d/0B4ZoiZnocOaQNWVUTWU2OUxfU2s/view?usp=sharing Histogram with all windows: https://drive.google.com/file/d/0B4ZoiZnocOaQRFp6U05xUXI2a0E/view?usp=sharing PMF curve with excluded windows: https://drive.google.com/open?id=0B4ZoiZnocOaQdGpQMkpDX0V6c1E Histogram with excluded windows: https://drive.google.com/open?id=0B4ZoiZnocOaQQnVRMV9Zc0tDcFU Can you give me some insight about why this is happening? Thank you very much for your help. Best regards, *Zeynep ABALI* MSc Candidate in Biomedical Sciences and Engineering -- 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.
