PIRSA:13120031

Improving the Martini model: coarse-graining with dynamic charges and polarization

APA

Khalak, Y. (2013). Improving the Martini model: coarse-graining with dynamic charges and polarization. Perimeter Institute. https://pirsa.org/13120031

MLA

Khalak, Yuriy. Improving the Martini model: coarse-graining with dynamic charges and polarization. Perimeter Institute, Dec. 05, 2013, https://pirsa.org/13120031

BibTex

          @misc{ pirsa_13120031,
            doi = {},
            url = {https://pirsa.org/13120031},
            author = {Khalak, Yuriy},
            keywords = {},
            language = {en},
            title = {Improving the Martini model: coarse-graining with dynamic charges and polarization},
            publisher = {Perimeter Institute},
            year = {2013},
            month = {dec},
            note = {PIRSA:13120031 see, \url{https://pirsa.org}}
          }
          

Yuriy Khalak University of Waterloo

Abstract

While successfully reproducing hydrophobic and hydrophilic interactions the Martini model is insufficient to keep a protein folded as it lacks electrostatic interactions. Using split charge equilibration at each time step can yield realistic dynamic bead charges. Combining this with a Drude oscillator based polarization model for all beads will permit modeling of hydrogen bonds to maintain secondary protein structure and will enable more accurate coarse-grained simulations of protein-protein and protein-membrane interactions.