Data provided by National Institute of Standards and Technology
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.
About this Dataset
Updated: 2025-04-06
Metadata Last Updated:
2024-11-18 00:00:00
Date Created:
N/A
Data Provided by:
Dataset Owner:
N/A
| Title | LAMMPS Simulation Data of Alchemical Processes |
|---|---|
| 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. |
| Modified | 2024-11-18 00:00:00 |
| Publisher Name | National Institute of Standards and Technology |
| Contact | mailto:[email protected] |
| Keywords | alchemical , alchemistry , MBAR , BAR , Bennett Acceptance Ratio , Thermodynamic Integration , LAMMPS |
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"modified": "2024-11-18 00:00:00",
"publisher": {
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"name": "National Institute of Standards and Technology"
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"theme": [
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"MBAR",
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"Bennett Acceptance Ratio",
"Thermodynamic Integration",
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]
}
