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Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond
A M Mathiowetz1, A Jain, N Karasawa
1Division of Chemistry and Chemical Engineering (CN 8921), Materials and Molecular Simulation Center, Beckman Institute (139-74), California.
Proteins
|November 1, 1994
Summary
Two new computational methods, Newton-Euler Inverse Mass Operator (NEIMO) dynamics and Cell Multipole Method (CMM), enable efficient molecular dynamics simulations for very large protein systems. These advancements allow for faster calculations and larger time steps, advancing the study of complex biological structures like viral capsids.
Area of Science:
- Computational Biology
- Biophysics
- Structural Biology
Background:
- Molecular dynamics simulations are crucial for understanding protein behavior.
- Simulating very large proteins using traditional Cartesian coordinates is computationally intensive.
- Internal coordinate methods offer advantages but face challenges with computational complexity.
Purpose of the Study:
- To introduce and validate two novel computational methods for large-scale molecular dynamics simulations.
- To demonstrate the applicability of these methods to complex protein systems, including viral capsids.
- To assess the computational efficiency and accuracy of the new methods.
Main Methods:
- Newton-Euler Inverse Mass Operator (NEIMO) dynamics: An order N algorithm for efficient internal coordinate calculations.
- Cell Multipole Method (CMM): A linear-scaling method for accurate non-bonded force calculations.
- Application to a range of protein systems, including the Tomato Bushy Stunt Virus (TBSV) capsid (488,000 atoms).
Main Results:
- NEIMO dynamics enables simulations of million-atom systems by directly calculating torsional accelerations.
- CMM provides accurate Coulomb and van der Waals interactions with linear computational cost.
- Both methods exhibit linear scaling of computational time with system size.
- Simulations of TBSV showed protein contraction in both normal and high pH forms.
Conclusions:
- NEIMO dynamics and CMM significantly advance the feasibility of simulating large biological macromolecules.
- These methods allow for larger time steps in molecular dynamics, improving simulation efficiency.
- The study successfully applies these techniques to a large viral capsid, demonstrating their power.