Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin....In my system rna is binding with gold nanoparticle...to find out the binding energy i run the umbrella sampling using the space 0.2 nm and i got total 59 configurations, each configuration was run for 5 ns. The profile files are shared with the link below.
https://www.dropbox.com/s/c8tj2rhu620xkim/Slide1.JPG?dl=0 https://www.dropbox.com/s/745kixwrfvguyyt/Slide2.JPG?dl=0 In the profile image, i have not got the plateu value, can i take the difference between final and starting pmf values for the binding enrgy. Please give suggestions. regards M.SathishKumar -- 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.
