How Accurate Does Newton Have to Be?

Autor: Carl Christian Kjelgaard Mikkelsen, Lorién López-Villellas, Pablo García-Risueño

Publikováno v: Parallel Processing and Applied Mathematics ISBN: 9783031304415

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::9d842f005dfdd4f2508f723afba38228
https://doi.org/10.1007/978-3-031-30442-2_1

Accurate and efficient constrained molecular dynamics of polymers through Newton’s method and special purpose code

Autor: Lorién López-Villellas, Carl Christian Kjelgaard Mikkelsen, Juan José Galano-Frutos, Santiago Marco-Sola, Jesús Alastruey-Benedé, Pablo Ibáñez, Miquel Moretó, Javier Sancho, Pablo García-Risueño

In molecular dynamics simulations we can often increase the time step by imposing constraints on internal degrees of freedom, such as bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of ph

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::6ea6b3f72c9408baa01678ec3b924e90
https://doi.org/10.1101/2022.09.28.509839

An Exact Expression to Calculate the Derivatives of Position-Dependent Observables in Molecular Simulations with Flexible Constraints

Autor: Pablo Echenique, Claudio N. Cavasotto, Monica De Marco, Pablo García-Risueño, J. L. Alonso

Publikováno v: PLoS ONE
PLoS ONE, Vol 12, Iss 12, p e0189454 (2017)

In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the constrained coordinates are fixed to configu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bd0ce8490ee1ccca9002e2593cfe5a83
https://pubmed.ncbi.nlm.nih.gov/21931757

Accelerating Sparse Arithmetic in the Context of Newton's Method for Small Molecules with Bond Constraints

Autor: Jesús Alastruey-Benedé, Carl Christian Kjelgaard Mikkelsen, Pablo García Risueño, Pablo Ibáñez-Marín

Publikováno v: Parallel Processing and Applied Mathematics ISBN: 9783319321486
PPAM (1)

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 accelerate Newton's method for solving the constraint equations for a sys

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6fc0a42eeea5587b29f06f8c55293261
http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-135304

Recent Memory and Performance Improvements in OCTOPUS Code

Autor: Fernando Nogueira, A. Arruabarrena, Angel Rubio, Joseba Alberdi-Rodriguez, Javier Muguerza, Pablo García-Risueño, Micael J. T. Oliveira

Publikováno v: Computational Science and Its Applications – ICCSA 2014
Lecture Notes in Computer Science
Computational Science and Its Applications – ICCSA 2014 ISBN: 9783319091464
ICCSA (4)

In this work we present the improvements made to the Octopus code in order to reduce the memory requirements and to optimise parallel data distribution. Both topics are central for efficiency and feasibility of calculations when the system must be ru

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dc29eabc2f0e3f277dbbc276490f477e
https://hdl.handle.net/11858/00-001M-0000-0024-140A-521.11116/0000-0005-3FD1-911858/00-001M-0000-0023-C409-A