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Python Package for Generating LAMMPS Input Scripts for Alchemical Processes: generate_alchemical_lammps_inputs

Metadata Updated: July 9, 2025

The parsers featured in this module are constructed to parse LAMMPS output files, (i.e., dump files), containing data for given potential energy values (an approximation of the Hamiltonian), U_{𝞴,𝞴'}, at specified values of 𝞴 and 𝞴', where varies from one to zero scaling the potential between solute and solvent in a reversible manner. The system is equilibrated at a 𝞴-state and energy values are evaluated at alternative 𝞴 values denotes by, 𝞴'. Because generating the input files can be cumbersome, functions have been included to generate the appropriate sections. This includes input scripts that generate formatted output files for the case where U has a separable dependence on 𝞴 or for analysis using thermodynamic integration (TI), Bennett Acceptance Ratio (BAR), and Multi-state Bennett Acceptance Ratio (MBAR). These resulting output files are generally formatted text files which can be readily analyzed using the python package, alchemlyb. An example is available for benzene solvated in water and a solvated Lennard-Jones dimer [DOI: 10.18434/mds2-3637]. Certain commercial equipment, instruments, or materials are identified in this paper to foster understanding. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the materials or equipment identified are necessarily the best available for the purpose.

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Public: This dataset is intended for public access and use. License: See this page for license information.

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Dates

Metadata Created Date July 9, 2025
Metadata Updated Date July 9, 2025
Data Update Frequency irregular

Metadata Source

Harvested from NIST

Additional Metadata

Resource Type Dataset
Metadata Created Date July 9, 2025
Metadata Updated Date July 9, 2025
Publisher National Institute of Standards and Technology
Maintainer
Identifier ark:/88434/mds2-3641
Data First Published 2025-03-11
Language en
Data Last Modified 2024-11-21 00:00:00
Category Chemistry:Theoretical chemistry and modeling
Public Access Level public
Data Update Frequency irregular
Bureau Code 006:55
Metadata Context https://project-open-data.cio.gov/v1.1/schema/data.json
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id 27efcb98-9534-4ba6-b676-f97b6e27b16b
Harvest Source Id 74e175d9-66b3-4323-ac98-e2a90eeb93c0
Harvest Source Title NIST
Homepage URL https://data.nist.gov/od/id/mds2-3641
License https://www.nist.gov/open/license
Program Code 006:045
Source Datajson Identifier True
Source Hash 363ce1a68bfdbc10e1d06c1f64e1f62305df17e1036ff6ecfd6397582b158ad4
Source Schema Version 1.1

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