Practical modeling of molecular systems with symmetries

Sergei Grudinin 1 Stephane Redon 1
1 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, LJK - Laboratoire Jean Kuntzmann, INPG - Institut National Polytechnique de Grenoble
Abstract : A new method for efficient modeling of macromolecular systems with symmetries is presented. The method is based on a hierarchical representation of the molecular system and a novel fast binary tree-based neighbor list construction algorithm. The method supports all types of molecular symmetry, including crystallographic symmetry. Testing the proposed neighbor list construction algorithm on a number of different macromolecular systems containing up to about 200,000 of atoms shows that (1) the current binary tree-based neighbor list construction algorithm scales linearly in the number of atoms for the central subunit, and sublinearly for its replicas, (2) the overall computational overhead of the method for a system with symmetry with respect to the same system without symmetry scales linearly with the cutoff value and does not exceed 50% for all but one tested macromolecules at the cutoff distance of 12 Å. (3) the method may help produce optimized molecular structures that are much closer to experimentally determined structures when compared with the optimization without symmetry, (4) the method can be applied to models of macromolecules with still unknown detailed structure.
Document type :
Journal articles
Complete list of metadatas

https://hal.archives-ouvertes.fr/hal-00748028
Contributor : Nano-D Equipe <>
Submitted on : Saturday, November 3, 2012 - 4:40:10 PM
Last modification on : Tuesday, May 21, 2019 - 11:48:13 AM

Links full text

Identifiers

Citation

Sergei Grudinin, Stephane Redon. Practical modeling of molecular systems with symmetries. Journal of Computational Chemistry, Wiley, 2010, 31 (9), pp.1799-1814. ⟨10.1002/jcc.21434⟩. ⟨hal-00748028⟩

Share

Metrics

Record views

372