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 by pulling one end of the siRNA untill it unbind from gold nanoparticle. The snap shots obtained from pulling simulation were used to generate configurations with the spacing 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.
