Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field

Autor: Qiu, Yudong, Smith, Daniel GA, Boothroyd, Simon, Jang, Hyesu, Hahn, David F, Wagner, Jeffrey, Bannan, Caitlin C, Gokey, Trevor, Lim, Victoria T, Stern, Chaya D, Rizzi, Andrea, Tjanaka, Bryon, Tresadern, Gary, Lucas, Xavier, Shirts, Michael R, Gilson, Michael K, Chodera, John D, Bayly, Christopher I, Mobley, David L, Wang, Lee-Ping

Publikováno v: Journal of chemical theory and computation, vol 17, iss 10

We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::b853828977c8c1113acb0f5fb965c464
https://escholarship.org/uc/item/46t0b6zt

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.

Autor: Dommer A; UC San Diego, La Jolla, CA, USA., Casalino L; UC San Diego, La Jolla, CA, USA., Kearns F; UC San Diego, La Jolla, CA, USA., Rosenfeld M; UC San Diego, La Jolla, CA, USA., Wauer N; UC San Diego, La Jolla, CA, USA., Ahn SH; UC San Diego, La Jolla, CA, USA., Russo J; Oregon Health & Science University, Portland, OR, USA., Oliveira S; University of Bristol, UK., Morris C; UC San Diego, La Jolla, CA, USA., Bogetti A; University of Pittsburgh, Pittsburgh, PA, USA., Trifan A; Argonne National Laboratory, Lemont, IL, USA.; University of Illinois at Urbana-Champaign, Urbana, IL, USA., Brace A; Argonne National Laboratory, Lemont, IL, USA.; University of Chicago, Chicago, IL, USA., Sztain T; UC San Diego, La Jolla, CA, USA.; Freie Universitat Berlin., Clyde A; Argonne National Laboratory, Lemont, IL, USA.; University of Chicago, Chicago, IL, USA., Ma H; Argonne National Laboratory, Lemont, IL, USA., Chennubhotla C; University of Pittsburgh, Pittsburgh, PA, USA., Lee H; Brookhaven National Lab and Rutgers University., Turilli M; Brookhaven National Lab and Rutgers University., Khalid S; University of Oxford, UK., Tamayo-Mendoza T; Entos, Inc., San Diego, CA, USA., Welborn M; Entos, Inc., San Diego, CA, USA., Christensen A; Entos, Inc., San Diego, CA, USA., Smith DG; Entos, Inc., San Diego, CA, USA., Qiao Z; California Institute of Technology, Pasadena, CA, USA., Sirumalla SK; Entos, Inc., San Diego, CA, USA., O'Connor M; Entos, Inc., San Diego, CA, USA., Manby F; Entos, Inc., San Diego, CA, USA., Anandkumar A; California Institute of Technology, Pasadena, CA, USA.; NVIDIA Corp, Santa Clara, CA, USA., Hardy D; University of Illinois at Urbana-Champaign, Urbana, IL, USA., Phillips J; University of Illinois at Urbana-Champaign, Urbana, IL, USA., Stern A; NVIDIA Corp, Santa Clara, CA, USA., Romero J; NVIDIA Corp, Santa Clara, CA, USA., Clark D; NVIDIA Corp, Santa Clara, CA, USA., Dorrell M; Pittsburgh Supercomputing Center, Pittsburgh, PA, USA., Maiden T; Pittsburgh Supercomputing Center, Pittsburgh, PA, USA., Huang L; Texas Advanced Computing Center, Austin, TX, USA., McCalpin J; Texas Advanced Computing Center, Austin, TX, USA., Woods C; University of Bristol, UK., Gray A; NVIDIA Corp, Santa Clara, CA, USA., Williams M; University of Bristol, UK., Barker B; Oracle for Research, Austin, TX, USA., Rajapaksha H; Oracle for Research, Austin, TX, USA., Pitts R; Oracle for Research, Austin, TX, USA., Gibbs T; NVIDIA Corp, Santa Clara, CA, USA., Stone J; University of Illinois at Urbana-Champaign, Urbana, IL, USA.; NVIDIA Corp, Santa Clara, CA, USA., Zuckerman DM; Oregon Health & Science University, Portland, OR, USA., Mulholland AJ; University of Bristol, UK., Miller T 3rd; Entos, Inc., San Diego, CA, USA.; California Institute of Technology, Pasadena, CA, USA., Jha S; Brookhaven National Lab and Rutgers University., Ramanathan A; Argonne National Laboratory, Lemont, IL, USA., Chong L; University of Pittsburgh, Pittsburgh, PA, USA., Amaro RE; UC San Diego, La Jolla, CA, USA.

Publikováno v: The international journal of high performance computing applications [Int J High Perform Comput Appl] 2023 Jan; Vol. 37 (1), pp. 28-44. Date of Electronic Publication: 2022 Oct 02.