ArticleJournal of computational chemistry2014
GneimoSim: a modular internal coordinates molecular dynamics simulation package.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.Journal of chemical theory and computation · 2017Article
- Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα.The Journal of biological chemistry · 2017Article
- Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.The Journal of chemical physics · 2016Article
- Internal coordinate molecular dynamics: a foundation for multiscale dynamics.The journal of physical chemistry. B · 2015Article
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Authors and funding
6 authors.
Funding
Abstract
The generalized Newton-Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials.
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Registered trials
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