LAMMPS datasets

Simulation datasets in any form.

The alchemtest.lammps module features datasets generated using the LAMMPS molecular dynamics engine. They can be accessed using the following accessor functions:

`load_benzene`()	Load data set of benzene in water.
`load_lj_dimer`()	Load data set of LJ dimer in solvent.

Simple TI and FEP

The data sets contain derivatives of the Hamiltonian (TI) and free energy perturbation (FEP) data suitable for processing with FEP estimators as well as BAR/MBAR. Individual \(\lambda\) windows were run independently.

LAMMPS: Benzene in Water

Benzene in water, alchemically decoupled to benzene in vacuum separated from bulk water

Test using LAMMPS dump files turned into u_nk and dHdl dataframes that could be calculated with MBAR or TI.

Notes

Data Set Characteristics:

Number of Legs:: 3 (Coulomb1 (NPT turn off Benzene charges), VDW (NPT), Coulomb2 (NVT turn on Benzene charges in vacuum))
Number of Windows:: 6 for Coulomb1, 16 for VDW, 6 for Coulomb2
Length of Windows:: 5ns
System Size:: 1668 atoms
Temperature:: 300 K
Pressure:: 1 bar
Alchemical Pathway:: vdw + coul –> vdw –> vacuum
Experimental Hydration Free Energy:: -0.90 +- 0.2 kcal/mol
Missing Values:: None
Energy unit:: kcal/mol
Time unit:: fs
Creator:: Jennifer A. Clark
Donor:: Jennifer A. Clark
Date:: Dec. 2024
License:: NIST
DOI:: 10.18434/mds2-3637

This dataset was provided by @jaclark5 on NIST MIDAS

Experimental value sourced from [Mobley2013].

[Mobley2013]

Mobley, David L. (2013). Experimental and Calculated Small Molecule Hydration Free Energies. UC Irvine: Department of Pharmaceutical Sciences, UCI. Retrieved from: http://escholarship.org/uc/item/6sd403pz

alchemtest.lammps.load_benzene()[source]

Load data set of benzene in water.

Returns:

data – Dictionary-like object, the interesting attributes are:

’data’ : the data files from lammps dump output
- ”mbar”: Files formatted for BAR or MBAR
  ’1_coul-off’: NPT removal of benzene’s charges
  
  ’2_vdw’: NPT decoupling of vdw forces between benzene and water
  
  ’3_coul-on’: NVT in vacuum restoration of benzene’s charges
- ”ti”
  ’1_coul-off’: NPT removal of benzene’s charges
  
  ’2_vdw’: NPT decoupling of vdw forces between benzene and water
  
  ’3_coul-on’: NVT in vacuum restoration of benzene’s charges
’DESCR’: the full description of the dataset

Return type:

Bunch

LAMMPS: LJ Dimer in Solvent

LJ Dimer in solvent, alchemically decoupled to a dimer in vacuum separated from bulk solvent

Test using LAMMPS dump files with PE to be turned into u_nk and dHdl dataframes that could be calculated with MBAR or TI.