orlandoacevedo / DES

Deep eutectic solvent force field parameters (OPLS-DES)

Deep eutectic solvent force field parameters (OPLS-DES)

Orlando Acevedo, University of Miami

This repository holds a set of OPLS-AA parameters for use in deep eutectic solvent simulations.

OPLS-AA force field parameters (OPLS-DES). Please see the following references for technical details:

1. doi:10.1021/acs.jpcb.8b06647
2. doi:10.1021/acs.jctc.1c00047

IMPORTANT: Hydrogen bond donor (HBD) parameters should NOT be used for pure organic liquid simulations! HBD parameters were specifically parameterized to work exclusively with the provided ion pairs in a DES environment.

Requirements

• Gromacs 5.0.7
  • Tested with CUDA 7.5/8.0 and on CentOS 6.5/7.0
  • Heat capacity DoS calculations (g_dos) requires Gromacs 5.1.4 due to a known bug in version 5.0.7

Download

git clone git://github.com/orlandoacevedo/DES.git

Parameters Available

• Ions

  • choline
  • chloride
  • ethylammonium
  • N,N-diethylethanolammonium
  • N-ethyl-N,N-dimethylethanolammonium

• Hydrogen bond donors

  • urea
  • glycerol
  • phenol
  • ethylene glycol
  • levulinic acid
  • oxalic acid
  • malonic acid
  • acetamide
  • 2,2,2-trifluoroacetamide

• DES - OPLS-DES bonded and nonbonded parameters

  • itp, top, and pdb folders

Tutorial

A brief tutorial is provided in the CCU-Tutorial directory. A README file will guide the user through the contruction of a CCU (reline) box using the OPLS-DES parameter set and a subsequent MD simulation. GROMACS input and output files are provided. The user is guided on how to compute the density of the deep eutetic solvent system.

References

Doherty, B.; Acevedo, O. "OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents" J. Phys. Chem. B, 2018, 122, 9982-9993. doi:10.1021/acs.jpcb.8b06647

• Featured on the journal cover Nov. 1, 2018 issue

Zhong, X.; Velez, C.; Acevedo, O. "Partial Charges Optimized by Genetic Algorithms for Deep Eutectic Solvent Simulations" J. Chem. Theory Comput., 2021, 17, 3078–3087. doi:10.1021/acs.jctc.1c00047

Velez, C.; Acevedo, O. "Simulation of Deep Eutectic Solvents: Progress to Promises" WIREs Comput. Mol. Sci., 2022, 12, e1598. doi:10.1002/wcms.1598

Rukmani, S.J.; Doherty, B.; Acevedo, O.; Colina, C.M. "Molecular simulations of deep eutetic solvents: A perspective on structure, dynamics, and physical properties" Rev. Comput. Chem., 2022, 32, 135-216. doi:doi.org/10.1002/9781119625933.ch4

About

Contributing Authors: Brian Doherty, Caroline Velez, Xiang Zhong, and Orlando Acevedo*

Funding: Gratitude is expressed to the National Science Foundation (NSF CHE-1562205 and CHE-2102038) for funding the project.

Software License: OPLS-DES. Copyright (C) 2021 Orlando Acevedo

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. http://www.gnu.org/licenses/