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 the conformational space along 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 Berger<\/strong> force field for lipids is a united atom (UA) force field extensively tested on DPPC membrane model against experimental data such as lipid densities and heat vaporizations. Lennard-Jones parameters of hydrocarbon chains were tuned with quantum chemical calculations on simple alcanes.<\/p>\r\n\r\n GROMOS S53A6<\/strong> force field is a united atom (UA) force field parametrized for a broad range of biomolecular systems. Parametrization procedure is focused on reproducing free enthalpies of solvation on a variety of compounds.<\/p>\r\n\r\n
\r\n <\/p>\r\n","categories":[{"id":12,"title":"United atoms MD","breadcrumb":[{"id":6,"title":"Simulated"},{"id":12,"title":"United atoms MD"}]}],"url":"https:\/\/molmedb.upol.cz\/api\/v1\/methods\/26","landing_page":"https:\/\/molmedb.upol.cz\/method\/26","created_at":"2018-06-30T18:36:30.000000Z","updated_at":"2019-07-19T07:14:04.000000Z"}}