Hi all, I am trying to pull a DNA molecule out of its binding pocket in a protein. I took Justin Lemkul's tutorial as the guiding script and started with k1 value of 1000. As it seemed, it needed more force to detach the molecule from its binding partner. Can you tell me how to estimate/calculate this value or it simply based on the trial-and-error method?
Also, what problems can take place if the value is large (huge, I guess)? Thanks, Souparno Adhikary University of Calcutta. -- 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.
