ArticleThe Journal of chemical physics2014
A simple molecular mechanics integrator in mixed rigid body and dihedral angle space.
Article in The Journal of chemical physics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Antibody binding modulates the dynamics of the membrane-bound prion protein.Biophysical journal · 2022Article
- Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins.Protein engineering, design & selection : PEDS · 2019Article
- Model reduction of rigid-body molecular dynamics via generalized multipole potentials.Physical review. E · 2019Article
- Article
- Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.Journal of chemical theory and computation · 2019Article
- Article
- Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.Journal of chemical theory and computation · 2017Article
- Dynamic microfluidic control of supramolecular peptide self-assembly.Nature communications · 2016Article
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Authors and funding
2 authors.
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Abstract
We propose a numerical scheme to integrate equations of motion in a mixed space of rigid-body and dihedral angle coordinates. The focus of the presentation is biomolecular systems and the framework is applicable to polymers with tree-like topology. By approximating the effective mass matrix as diagonal and lumping all bias torques into the time dependencies of the diagonal elements, we take advantage of the formal decoupling of individual equations of motion. We impose energy conservation independently for every degree of freedom and this is used to derive a numerical integration scheme. The cost of all auxiliary operations is linear in the number of atoms. By coupling the scheme to one of two popular thermostats, we extend the method to sample constant temperature ensembles. We demonstrate that the integrator of choice yields satisfactory stability and is free of mass-metric tensor artifacts, which is expected by construction of the algorithm. Two fundamentally different systems, viz., liquid water and an α-helical peptide in a continuum solvent are used to establish the applicability of our method to a wide range of problems. The resultant constant temperature ensembles are shown to be thermodynamically accurate. The latter relies on detailed, quantitative comparisons to data from reference sampling schemes operating on exactly the same sets of degrees of freedom.
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