Dear GMX-users In an old post in this list about umbrella sampling in gromacs and the pull code, ( http://gromacs.org_gmx-users.maillist.sys.kth.narkive.com/w3NmJ69y/md-pull-code-in-umbrella-sampling ) Christopher Neale gave an interesting comment about the case of pulling a ligand out of a protein, especially when some of first contacts between the two pull groups can cause improper sampling as they need other orthogonal X/Y degrees of freedom
his suggested solution was as follows: "Personally, I would solve this by adding a second pull group with a flat-bottom potential that acts only on X and Y to keep the drug within a cylinder that extends along Z away from your protein. However, you would need to modify gromacs source code for this (I have some posts on the uses lists over the years about how to do this). An alternative solution is to define an order parameter that acts in all 3 dimensions, although you may need to compute the free energy of releasing this restraint (a) in the binding pocket and (b) at large separations where your PMF flattens out to zero." I would like to ask Christopher or other expert users here to explain more about these solutions, especially which one of them is easier? -- Suhaib Shekfeh Department of Pharmaceutical Chemistry Gazi University Eczailik Fakültesi (Faculty of Pharmacy) LinkedIn : http://www.linkedin.com/pub/suhaib-shekfeh/b/65a/255 -- 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.
