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MSCALE: A General Utility for Multiscale Modeling | JoVE Visualize

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Mathematical Sciences

MSCALE: A General Utility for Multiscale Modeling

H Lee Woodcock¹, Benjamin T Miller, Milan Hodoscek

¹Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., CHE205, Tampa, FL 33620-5250.

Journal of Chemical Theory and Computation|June 22, 2011

View abstract on PubMed

Summary

This study introduces MSCALE, a new framework for multiscale modeling in macromolecular simulations. It integrates various theoretical models, enabling more comprehensive biochemical problem-solving with enhanced computational efficiency.

Area of Science:

Computational chemistry
Biophysics
Theoretical chemistry

Background:

Multiscale modeling is crucial for complex biochemical problems.
Existing methods often lack flexibility in combining different theoretical scales.

Purpose of the Study:

To introduce MSCALE, a generalized framework for concurrent multiscale calculations.
To implement MSCALE within the CHARMM package for enhanced macromolecular modeling.

Main Methods:

Developed a parallelized framework (MSCALE) supporting additive and subtractive schemes.
Integrated quantum mechanics/molecular mechanics (QM/MM), classical force fields, and coarse-grained models.
Utilized Message Passing Interface (MPI) for parallel computation and external program integration.

Main Results:

Demonstrated MSCALE's utility with QM/MM, QM/QM, multi-force field, and mixed-resolution simulations.
Enabled integration with external packages like AMBER and TINKER.
Successfully performed normal mode analysis on mixed-resolution systems.

Conclusions:

MSCALE provides a versatile and efficient platform for advanced multiscale simulations.
The framework facilitates the combination of diverse computational approaches.
Future work will address mathematical challenges and further improvements.

Applied Mathematics

Complex Systems

Mscale: A General Utility For Multiscale Modeling