ArticleThe Journal of chemical physics2012
Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.
Article in The Journal of chemical physics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
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- On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins.Journal of computational chemistry · 2021Article
- Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.Journal of chemical theory and computation · 2017Article
- Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations.Scientific reports · 2017Article
- Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.PLoS computational biology · 2016Article
- Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.Biochimica et biophysica acta · 2015Article
- Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.The journal of physical chemistry. A · 2015Article
- Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.Journal of chemical theory and computation · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency.
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