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LAMMPS Simulation Data of Alchemical Processes

Published by National Institute of Standards and Technology | National Institute of Standards and Technology | Catalog Last Checked: September 02, 2026 at 07:19 PM | Dataset Last Updated: November 18, 2024
This data includes a four alchemical processes with data files generated with the python package: generate_alchemical_lammps (DOI from MIDAS) and the resulting output to be used for the calculation of free energies using Multi-state Bennett Acceptance Ratio (MBAR), BAR, or Thermodynamic Integration (TI). These input files are only applicable for LAMMPS versions after April 2024. The four cases can be separated into two systems, benzene solvated in water, and a Lennard-Jones (LJ) dimer in solvent. These four cases are: 1) benzene 1: In the NPT ensemble, scale the charges of benzene atoms from full values to zero over six steps. 2) benzene 2: In the NPT ensemble, scale the van der Waals potential between benzene and water from full values to zero over sixteen steps. 3) benzene 3: In the NVT ensemble with benzene in vacuum, scale the charges of benzene's atoms from zero to full values over six steps. 4) lj_dimer: In the NPT ensemble, change the cross interaction energy parameter between solvent and dimer from a value of 1 to 2.

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@type dcat:Dataset
accessLevel public
accrualPeriodicity irregular
bureauCode 
[
  "006:55"
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contactPoint 
{
  "fn": "Debra Audus",
  "hasEmail": "mailto:debra.audus@nist.gov"
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description This data includes a four alchemical processes with data files generated with the python package: generate_alchemical_lammps (DOI from MIDAS) and the resulting output to be used for the calculation of free energies using Multi-state Bennett Acceptance Ratio (MBAR), BAR, or Thermodynamic Integration (TI). These input files are only applicable for LAMMPS versions after April 2024. The four cases can be separated into two systems, benzene solvated in water, and a Lennard-Jones (LJ) dimer in solvent. These four cases are: 1) benzene 1: In the NPT ensemble, scale the charges of benzene atoms from full values to zero over six steps. 2) benzene 2: In the NPT ensemble, scale the van der Waals potential between benzene and water from full values to zero over sixteen steps. 3) benzene 3: In the NVT ensemble with benzene in vacuum, scale the charges of benzene's atoms from zero to full values over six steps. 4) lj_dimer: In the NPT ensemble, change the cross interaction energy parameter between solvent and dimer from a value of 1 to 2.
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]
identifier ark:/88434/mds2-3637
issued 2024-12-30
keyword 
[
  "BAR",
  "Bennett Acceptance Ratio",
  "LAMMPS",
  "MBAR",
  "Thermodynamic Integration",
  "alchemical",
  "alchemistry"
]
landingPage https://data.nist.gov/od/id/mds2-3637
language 
[
  "en"
]
license https://www.nist.gov/open/license
modified 2024-11-18 00:00:00
programCode 
[
  "006:045"
]
publisher 
{
  "name": "National Institute of Standards and Technology",
  "@type": "org:Organization"
}
theme 
[
  "Chemistry:Chemical thermodynamics and chemical properties",
  "Chemistry:Theoretical chemistry and modeling"
]
title LAMMPS Simulation Data of Alchemical Processes

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