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Theoretical and Computational Chemistry

Working Paper

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

Vinicius Cruzeiro, Madushanka Manathunga, Kenneth M. Merz, Jr., Andreas Goetz

Version 1 posted 16 February 2021

1,897

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Biological and Medicinal Chemistry

Working Paper

A Fast Implementation of the Nudged Elastic Band Method in AMBER

Delaram Ghoreishi, David Cerutti, Zachary Fallon, Carlos Simmerling, Adrian Roitberg

Version 1 posted 18 June 2019

799

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Theoretical and Computational Chemistry

Working Paper

Validation of AMBER/GAFF for Relative Free Energy Calculations

Lin Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.

Version 1 posted 04 February 2019

1,770

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2

Citations

Theoretical and Computational Chemistry

Working Paper

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

Vinicius Cruzeiro, Gustavo Troiano Feliciano, Adrian Roitberg

Version 1 posted 03 February 2020

449

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Theoretical and Computational Chemistry

Working Paper

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian, Koushik Kasavajhala, Kellon Belfon, Lauren Raguette, He Huang, Angela Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu, Carlos Simmerling

Version 1 posted 17 June 2019

2,285

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1

Citations

Biological and Medicinal Chemistry

Working Paper

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Thomas Fellowes, JONATHAN WHITE

Version 2 posted 05 May 2021

653

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Theoretical and Computational Chemistry

Working Paper

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

Klaudia Mrazikova, Jiri Sponer, Vojtech Mlynsky, Pascal Auffinger, Holger Kruse

Version 1 posted 15 September 2021

262

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Theoretical and Computational Chemistry

Working Paper

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Aliza Rubenstein, Kristin Blacklock, Hai Nguyen, David Case, Sagar Khare

Version 2 posted 04 April 2018

1,526

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Theoretical and Computational Chemistry

Working Paper

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Ido Ben-Shalom, Zhixiong Lin, Brian Radak, Charles Lin, Woody Sherman, Michael K. Gilson

Version 1 posted 20 July 2020

570

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1

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Theoretical and Computational Chemistry

Working Paper

QM/MM Simulations on NVIDIA and AMD GPUs

Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz, Jr

Version 1 posted 30 November 2022

430

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15 results in amber in Keywords: amber

Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK

A Fast Implementation of the Nudged Elastic Band Method in AMBER

Validation of AMBER/GAFF for Relative Free Energy Calculations

Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

QM/MM Simulations on NVIDIA and AMD GPUs

15 results in Keywords: amber