Paper Citing NAMD - Abstract
Doemer, Manuel; Maurer, Patrick; Campomanes, Pablo; Tavernelli, Ivano; Rothlisberger, Ursula
Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:412-422, JAN 2014
We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.
