Literature DB >> 19639948

DL-FIND: an open-source geometry optimizer for atomistic simulations.

Johannes Kästner1, Joanne M Carr, Thomas W Keal, Walter Thiel, Adrian Wander, Paul Sherwood.   

Abstract

Geometry optimization, including searching for transition states, accounts for most of the CPU time spent in quantum chemistry, computational surface science, and solid-state physics, and also plays an important role in simulations employing classical force fields. We have implemented a geometry optimizer, called DL-FIND, to be included in atomistic simulation codes. It can optimize structures in Cartesian coordinates, redundant internal coordinates, hybrid-delocalized internal coordinates, and also functions of more variables independent of atomic structures. The implementation of the optimization algorithms is independent of the coordinate transformation used. Steepest descent, conjugate gradient, quasi-Newton, and L-BFGS algorithms as well as damped molecular dynamics are available as minimization methods. The partitioned rational function optimization algorithm, a modified version of the dimer method and the nudged elastic band approach provide capabilities for transition-state search. Penalty function, gradient projection, and Lagrange-Newton methods are implemented for conical intersection optimizations. Various stochastic search methods, including a genetic algorithm, are available for global or local minimization and can be run as parallel algorithms. The code is released under the open-source GNU LGPL license. Some selected applications of DL-FIND are surveyed.

Entities:  

Year:  2009        PMID: 19639948     DOI: 10.1021/jp9028968

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  49 in total

1.  Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.

Authors:  Tai-Sung Lee; Brian K Radak; Ming Huang; Kin-Yiu Wong; Darrin M York
Journal:  J Chem Theory Comput       Date:  2014-01-14       Impact factor: 6.006

2.  VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.

Authors:  Erich R Kuechler; Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2016-04-28       Impact factor: 3.488

3.  Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation.

Authors:  Zhongyue Yang; Rimsha Mehmood; Mengyi Wang; Helena W Qi; Adam H Steeves; Heather J Kulik
Journal:  React Chem Eng       Date:  2018-11-29       Impact factor: 4.239

4.  A probabilistic approach for estimating water permeability in pressure-driven membranes.

Authors:  Linkel K Boateng; Ramin Madarshahian; Yeomin Yoon; Juan M Caicedo; Joseph R V Flora
Journal:  J Mol Model       Date:  2016-07-21       Impact factor: 1.810

5.  Molecular simulations of RNA 2'-O-transesterification reaction models in solution.

Authors:  Brian K Radak; Michael E Harris; Darrin M York
Journal:  J Phys Chem B       Date:  2012-12-24       Impact factor: 2.991

6.  The influence of base pair tautomerism on single point mutations in aqueous DNA.

Authors:  A Gheorghiu; P V Coveney; A A Arabi
Journal:  Interface Focus       Date:  2020-10-16       Impact factor: 3.906

7.  Reaction mechanism of the bicopper enzyme peptidylglycine α-hydroxylating monooxygenase.

Authors:  Enrique Abad; Judith B Rommel; Johannes Kästner
Journal:  J Biol Chem       Date:  2014-03-25       Impact factor: 5.157

8.  The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins.

Authors:  Katrin Röllen; Joachim Granzin; Alina Remeeva; Mehdi D Davari; Thomas Gensch; Vera V Nazarenko; Kirill Kovalev; Andrey Bogorodskiy; Valentin Borshchevskiy; Stefanie Hemmer; Ulrich Schwaneberg; Valentin Gordeliy; Karl-Erich Jaeger; Renu Batra-Safferling; Ivan Gushchin; Ulrich Krauss
Journal:  J Biol Chem       Date:  2021-04-13       Impact factor: 5.157

9.  What Is the Catalytic Mechanism of Enzymatic Histone N-Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field?

Authors:  Rajeev Ramanan; Sodiq O Waheed; Christopher J Schofield; Christo Z Christov
Journal:  Chemistry       Date:  2021-06-04       Impact factor: 5.020

10.  Machine learning based energy-free structure predictions of molecules, transition states, and solids.

Authors:  Dominik Lemm; Guido Falk von Rudorff; O Anatole von Lilienfeld
Journal:  Nat Commun       Date:  2021-07-22       Impact factor: 14.919

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.