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 AMBER Lipid14<\/strong> is the latest force field from AMBER Lipid force fields family, allowing membrane simulation without the need of using additional surface tension. This version of the force field was tested on six different lipid membrane types and is compatible with AMBER protein, nucleic acid, carbohydrates and small molecules force field.<\/p>\r\n\r\n AMBER ff99SB<\/strong> is an all atom (AA) force field with reparametrized phi\/psi dihedral terms in energy funcion to better represent secondary structure elements of protein backbone.<\/p>\r\n\r\n
\r\n <\/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\/29","landing_page":"https:\/\/molmedb.upol.cz\/method\/29","created_at":"2018-06-30T20:26:21.000000Z","updated_at":"2019-07-19T07:13:55.000000Z"}}