Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options.
I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other and have been crystallized in three different conformations. I want to calculate the change in binding energy of the two domains wrt change in their relative position, i.e. keeping position of one domain constant what is change in binding energy as the other domain moves from conformation 1, through conformation 2 to finally, conformation 3. What is the best way to do so? At first, I considered using umbrella sampling to address the problem. Here too, I was not sure how to write a pull code for such a complex reaction coordinate. Also, even if I can generate the conformations, what would be the ideal number of windows that would be needed to correctly generate a PMF ? My feeling is it would be a large number, but again it just a guess. Is there is a better way than this? Any help would be appreciated. Thanks in advance. Regards, Abhishek Acharya -- 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.
