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

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 physical phenomena that we can afford to simulate. I...

Full description

Saved in:
Bibliographic Details
Published in:bioRxiv 2022-09
Main Authors: López-Villellas, Lorién, Carl Christian Kjelgaard Mikkelsen, Galano-Frutos, Juan José, Marco-Sola, Santiago, Alastruey-Benedé, Jesús, Ibáñez, Pablo, Moretó, Miquel, Sancho, Javier, García-Risueño, Pablo
Format: Article
Language:English
Subjects:
Molecular Biology
Citations: Items that this one cites
Online Access:Request full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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 physical phenomena that we can afford to simulate. In this article we analyse the impact of the accuracy of the constraint solver. We present ILVES-PC, an algorithm for imposing constraints on proteins accurately and efficiently. Competing Interest Statement The authors have declared no competing interest.
ISSN:2692-8205
DOI:10.1101/2022.09.28.509839