Umbrella sampling<\/strong> is an enhanced sampling technique used in computational chemistry to predict energetical landscape by intensive sampling of conformational space. In calculations of permeation through membranes, a set of initial drug positions across the membrane is estimated. For each of those, a simulation is performed, restraining the drug in position with a harmonic potential to sample conformational space along the reaction coordinate. Using Weighted Histogram Analysis Method (WHAM), PMF is recovered and thermodynamic properties of drug membrane permeation are calculated.<\/p>\r\n\r\n CHARMM36 <\/strong>is an all atom (AA) force field for lipid simulation with redefined parameters for lipid headgroups (choline and ethanolamine) and both saturated and unsaturated lipid chains based on quantum mechanical and experimental data. Newly derived parameters were tested on fully hydrated bilayers. Parameters for sphingolipids were added.<\/p>\r\n","categories":[{"id":11,"title":"Atomistic MD","breadcrumb":[{"id":6,"title":"Simulated"},{"id":11,"title":"Atomistic MD"}]}],"url":"https:\/\/molmedb.upol.cz\/api\/v1\/methods\/31","landing_page":"https:\/\/molmedb.upol.cz\/method\/31","created_at":"2018-06-30T21:31:26.000000Z","updated_at":"2019-07-19T07:14:12.000000Z"}}