Cummins, Peter; Rostov, Ivan; Gready, Jill
We present a two-dimensional grid method for the calculation of complete free-energy surfaces for enzyme reactions using a hybrid quantum mechanical/molecular mechanical (QM/ MM) potential within the semiempirical (PM3) QM approximation. This implementation is novel in that parallel processing with multiple trajectories (replica-exchange molecular dynamics simulations) is used to sample configuration space. The free energies at each grid point are computed using the thermodynamic integration...[Show more]
Items in Open Research are protected by copyright, with all rights reserved, unless otherwise indicated.