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Foundation :: Bioinformatics :: GNEIMO

GNEIMO

Generalized Newton-Euler Inverse Mass Operator

Moderators:
Abhinandan Jain
Nagarajan Vaidehi
Total downloads from Open Channel to date: 36

In collaboration with Prof. Vaidehi's group at City of Hope, the DARTS spacecraft multibody dynamics engine has been adapted to develop the Generalized Newton-Euler Inverse Mass Operator (GNEIMO) software for the Molecular dynamics molecular dynamics simulation of large-scale molecular systems. GNEIMO is in use for the simulation and analysis of protein folding, drug design, virus mechanisms and other applications. Other computational chemistry applications include the study of biomolecular processes and for the modeling and design of new materials including polymers and catalysts.

GNEIMO works with internal coordinates molecular models obtained by fixing the high frequency modes. The internal coordinates model reduces the number of degrees of freedom from 3N (where N is the number of atoms) to N (the number of dihedral degrees of freedom). The equations of motion for internal coordinates model are coupled and involve a dense mass matrix. The conventional algorithm for solving constrained equations involves inversion of the dense mass matrix M with computational cost scaling as the cubic power of N. The GNEIMO method provides a O(N) algorithm for solving the same equations of motion.

The development of the O(N) GNEIMO algorithm was motivated by the impracticality of useful long time molecular dynamics of macromolecules using conventional O(N3) algorithms for contrained molecular dynamics. The speed performance of the GNEIMO method has large implications on the ability to perform large scale molecular dynamics on biologically relevant molecules and materials. This has been demonstrated using GNEIMO. Mathematical techiniqes from JPL's Spatial Operator Algebra framework were used to analytically pose the constrained molecular dynamics problem, and to develop a the fast O(N) algorithms for their solution.

The current version of the GNEIMO software supports torsional MD dynamics at constant temperature (NVT) ensemble and also at constant energy (NVE) ensemble. The three integrators supported in GNEIMO are: Lobatto, RK4 and CVODE. A time step of 5fs is recommended for most proteins with the Lobatto and RK4 integrators. CVODE is a variable step integrator that adaptively adjusts the time step during the simulation.

Please visit http://www.ncbi.nlm.nih.gov/pubmed/?term=abhinandan+jain for recent GNEIMO publications and details on the GNEIMO methods and algorithms. For feedback and comments, please email
gneimo dot software at list dot jpl dot nasa dot gov.


Copyright 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014 Caltech/Jet Propulsion Laboratory
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