[HTML][HTML] Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code
L López-Villellas, CCK Mikkelsen… - Computer Physics …, 2023 - Elsevier
In molecular dynamics simulations we can often increase the time step by imposing
constraints on bond lengths and bond angles. This allows us to extend the length of the time …
constraints on bond lengths and bond angles. This allows us to extend the length of the time …
Newton's method revisited: How accurate do we have to be?
CC Kjelgaard Mikkelsen… - Concurrency and …, 2024 - Wiley Online Library
We analyze the convergence of quasi‐Newton methods in exact and finite precision
arithmetic using three different techniques. We derive an upper bound for the stagnation …
arithmetic using three different techniques. We derive an upper bound for the stagnation …
The canonical equilibrium of constrained molecular models
P Echenique, CN Cavasotto… - The European Physical …, 2011 - Springer
In order to increase the efficiency of the computer simulation of biological molecules, it is
very common to impose holonomic constraints on the fastest degrees of freedom; normally …
very common to impose holonomic constraints on the fastest degrees of freedom; normally …
Linearly scaling direct method for accurately inverting sparse banded matrices
P García-Risueño, P Echenique - Journal of Physics A …, 2012 - iopscience.iop.org
In many problems in computational physics and chemistry, one finds special kinds of sparse
matrices, called banded matrices. These matrices, which are defined as having non-zero …
matrices, called banded matrices. These matrices, which are defined as having non-zero …
Accelerating sparse arithmetic in the context of Newton's method for small molecules with bond constraints
CCK Mikkelsen, J Alastruey-Benedé… - Parallel Processing and …, 2016 - Springer
Molecular dynamics is used to study the time evolution of systems of atoms. It is common to
constrain bond lengths in order to increase the time step of the simulation. Here we …
constrain bond lengths in order to increase the time step of the simulation. Here we …
[PDF][PDF] Método Paralelo de Resolución de Ecuaciones de Ligadura para Moléculas Lineales Parallel Constraint Solver for Linear Molecules
RL Benıtez - zaguan.unizar.es
La dinámica molecular es una técnica de simulación por computador que estudia la
evolución en el tiempo de un sistema de partıculas. Las herramientas que realizan estas …
evolución en el tiempo de un sistema de partıculas. Las herramientas que realizan estas …
Método paralelo de resolución de ecuaciones de ligadura para moléculas lineales
R Langarita Benítez, J Alastruey Benedé… - zaguan.unizar.es
La dinámica molecular es una técnica de simulación por computador que estudia la
evolución en el tiempo de un sistema de partículas. Las herramientas que realizan estas …
evolución en el tiempo de un sistema de partículas. Las herramientas que realizan estas …
Exact and efficient calculation of the derivatives of Lagrange multipliers for molecular dynamics simulations of biological molecules and polymers
P García-Risueño - Physica Scripta, 2019 - iopscience.iop.org
In the simulation of biological molecules and polymers, it is customary to impose constraints
on the fastest degrees of freedom so as to freeze their motion and increase the time step. An …
on the fastest degrees of freedom so as to freeze their motion and increase the time step. An …
[HTML][HTML] Computational method for highly constrained molecular dynamics of rigid bodies: Coarse-grained simulation of auxetic two-dimensional protein crystals
JA Campos-Gonzalez-Angulo, G Wiesehan… - The Journal of …, 2020 - pubs.aip.org
The increasing number of protein-based metamaterials demands reliable and efficient
theoretical and computational methods to study the physicochemical properties they may …
theoretical and computational methods to study the physicochemical properties they may …
Computational method for highly-constrained molecular dynamics of rigid bodies: coarse-grained simulation of auxetic two-dimensional protein crystals
JA Angulo, G Wiesehan, RF Ribeiro… - arXiv preprint arXiv …, 2017 - arxiv.org
The increasing number of protein-based metamaterials demands reliable and efficient
theoretical and computational methods to study the physicochemical properties they may …
theoretical and computational methods to study the physicochemical properties they may …