Advanced Electrostatic Computation in Molecular Dynamics

Information

  • Research Project
  • 6882566
  • ApplicationId
    6882566
  • Core Project Number
    R43GM073391
  • Full Project Number
    1R43GM073391-01
  • Serial Number
    73391
  • FOA Number
  • Sub Project Id
  • Project Start Date
    5/1/2005 - 19 years ago
  • Project End Date
    10/31/2006 - 17 years ago
  • Program Officer Name
    EDMONDS, CHARLES G.
  • Budget Start Date
    5/1/2005 - 19 years ago
  • Budget End Date
    10/31/2006 - 17 years ago
  • Fiscal Year
    2005
  • Support Year
    1
  • Suffix
  • Award Notice Date
    4/28/2005 - 19 years ago
Organizations

Advanced Electrostatic Computation in Molecular Dynamics

DESCRIPTION (provided by applicant): Advances in computational hardware and molecular modeling techniques have revolutionized our ability to simulate electrostatic interactions which play a fundamental role in the stability, structure, folding and function of bio-molecules. Currently, the continuum electrostatic description based upon the Poisson- Boltzmann Equation (PBE) offers the best combination of modeling fidelity and computational cost. While very large bio-molecular assemblies such as ribosomes, containing hundreds of thousands of atoms, have been successfully solved using PBE solvers, major difficulties are encountered when these solvers are incorporated into molecular dynamics (MD) and energy minimization (EM) codes. Impaired accuracy of predicted electrostatic field at molecular surfaces destabilizes MD simulations and hinders convergence in EM computations. The proposed effort will provide new computational tools to accurately and efficiently predict the required electrostatic properties near the molecular surface. Previous technology, notably a novel adaptive Cartesian grid structure that maximizes computational performance for large-scale bio-molecules, will be modified to achieve high accuracy at the surface. The resulting computational tool should prove invaluable to: (i) MD and EM calculations by efficiently providing high fidelity, PBE-quality electrostatic energy gradients and (ii) researchers interested in relating electrostatic surface properties (e.g., potential and induced charge) to bio-molecular function.

IC Name
NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
  • Activity
    R43
  • Administering IC
    GM
  • Application Type
    1
  • Direct Cost Amount
  • Indirect Cost Amount
  • Total Cost
    99822
  • Sub Project Total Cost
  • ARRA Funded
  • CFDA Code
    859
  • Ed Inst. Type
  • Funding ICs
    NIGMS:99822\
  • Funding Mechanism
  • Study Section
    ZRG1
  • Study Section Name
    Special Emphasis Panel
  • Organization Name
    CONTINUUM DYNAMICS, INC.
  • Organization Department
  • Organization DUNS
  • Organization City
    EWING
  • Organization State
    NJ
  • Organization Country
    UNITED STATES
  • Organization Zip Code
    08618
  • Organization District
    UNITED STATES