Development of accurate force fields for aqueous biological environments using a massively parallel multiscale approach
EMSL Project ID
30794
Abstract
The ability to calculate accurate energies and properties of large molecules with massively-parallel computers presents an extraordinary opportunity to develop new models for bonded and non-bonded interactions used in classical force fields by directly calculating such parameters from first principles electronic structure calculations. Since those force fields usually contain a large set of parameters, especially those that describe polarization, it becomes increasingly difficult to determine these parameters in a rigorous way using only experimental data. In contrast, quantum chemical calculations accurately determine force constants, charge distributions, and polarizabilities for the relevant moieties with well-known accuracy. The coupled-cluster method is universally accepted as the most accurate method for molecules near their equilibrium geometry, and the functionality to calculate all relevant properties for determining force fields is available within NWChem. Using NWChem on the new EMSL supercomputer, polarizable force field parameters will be determined using first principles for use in both classical and nuclear quantum statistical mechanical simulations. The use of those state-of-the-art quantum chemical methods for force field development will increase the accuracy and generality of existing models and contribute significantly to the development of a hierarchy of increasingly accurate models. The emergence of a Jacobs ladder of models for molecular simulations, in analogy to that in density functional theory [J. P. Perdew and K. Schmidt, in "Density Functional Theory and Its Application to Materials, edited by V. Van Doren, C. Van Alsenoy, and P. Geerlings (AIP, Melville, NY, 2001)], promises to make significant contributions to molecular simulations relevant to all four of EMSLs science themes. The open (non-proprietary) nature of this project ensures that it will have maximum impact on the user community for the respective models developed.
Project Details
Project type
Capability Research
Start Date
2008-10-11
End Date
2011-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
"Accurate dipole polarizabilities for water clusters n = 2--12 at the coupled-cluster level of theory and benchmarking of various density functionals"
Jeff R. Hammond, Niranjan Govind, Karol Kowalski, Jochen Autschbach, and Sotiris S. Xantheas, J. Chem. Phys. 131, 214103 (2009), DOI:10.1063/1.3263604
American Chemical Society National Meeting; Washington, DC (August 18th, 2009). "The challenging excited states of the membrane-bound fluorophore di-8-ANEPPS." (with Benoit Roux, Niri Govind and Karol Kowalski)
Hammond JR. 2009. "Coupled-cluster Response Theory and Accurate Electric-field Properties for Large Molecules." Presented by Jeff Hammond (Invited Speaker) at Theory Department, Fritz Haber Institute of the Max Planck Society, Berlin, Germany on July 26, 2009.
Hammond JR. 2009. "New Frontiers in Quantum Chemistry Using Supercomputers." Presented by Jeff Hammond (Invited Speaker) at CSCS User Day, Argonne, IL on September 11, 2009.
Hammond JR. 2010. "New Frontiers in Quantum Chemistry Using Supercomputers." Presented by Jeff Hammond (Invited Speaker) at Computation Institute, University of Chicago, IL on June 30, 2010.
Hammond JR. 2010. "New Frontiers in Quantum Chemistry Using Supercomputers." Presented by Jeff Hammond (Invited Speaker) at Head-Gordon Group Meeting, UC Berkeley, CA on January 22, 2010.
J. R. Hammond, Karl F. Freed, Sotiris S. Xantheas and K. Kowalski, poster presented at the American Chemical Society National Meeting, Spring 2009.
J. R. Hammond, poster presented at SciDAC 2009.
J. R. Hammond, presentation given at Harvard (Aspuru-Guzik group) May 2009.
J. R. Hammond, presentation given at SIAM-CSE (Miami, FL) March 2009.
J. R. Hammond, thesis defense presentation, May 2009.
J. R. Hammond, University of Chicago Doctoral Thesis (May 2009). "Coupled-cluster response theory: parallel algorithms and novel applications"
Kilyanek SM, EJ Stoebenau, N Vinayavekhin, and RF Jordan. 2010. "Mechanism of the Reaction of Vinyl Chloride with (a-diimine)PdMe+ Species." Organometallics 29(7):1750-1760. doi:10.1021/om1000925
K. Kowalski, S. Krishnamoorthy, O. Villa, J. R. Hammond, and N. Govind, J. Chem. Phys. 132, 154103 (2010). "Active-space completely-renormalized equation-of-motion coupled-cluster formalism: Excited-state studies of green fluorescent protein, free-base porphyrin, and oligoporphyrin dimer."
Paesani F, S Yoo, HJ Bakker, and SS Xantheas. 2010. "Nuclear Quantum Effects in the Reorientation of Water." The Journal of Physical Chemistry Letters 1(15):2316-2321. doi:10.1021/jz100734w
Sriram Krishnamoorthy, Sameer Shende, Jeff R. Hammond, Nichols A. Romero and Allen D. Malony, submitted to HiPC 2010. "NWChem Workload Characterization Using the TAU Performance System."
"The Melting Temperature of bulk silicon from ab initio molecular dynamics simulations"
Soohaeng Yoo, Sotiris S. Xantheas and Xiao Cheng Zeng
accepted to Chemical Physics Letters (2009)
doi:10.1016/j.cplett.2009.09.075
Wang XB, JC Werhahn, LS Wang, K Kowalski, A Laubereau, and SS Xantheas. 2009. "Observation of a remarkable temperature effect in the hydrogen bonding structure and dynamics of the CN-(H2O) cluster." Journal of Physical Chemistry A 113(35):9579-9584.
Yoo S, E Apra, XC Zeng, and SS Xantheas. 2010. "High-Level ab initio electronic structure calculations of Water Clusters (H2O)16 and (H2O)17: a new global minimum for (H2O)16." The Journal of Physical Chemistry Letters 1(20):3122-3127. doi:10.1021/jz101245s
Yoo S, MV Kirov, and SS Xantheas. 2009. "Low-energy networks of the T-cage (H2O)(24) cluster and their use in constructing periodic unit cells of the structure I (sl) hydrate lattice." Journal of the American Chemical Society 131(22):7564-7566.
Yoo S, XC Zeng, and SS Xantheas. 2009. "On the phase diagram of water with density functional theory potentials: the melting temperature of Ice I-h with the Perdew-Burke-Ernzerhof and Becke-Lee-Yang-Parr functionals." Journal of Chemical Physics 130(22):Art. No. 211102.