GOMC datasets
GOMC Monte Carlo simulation datasets.
The alchemlyb.gomc module features datasets generated using the
GPU Optimized Monte Carlo (GOMC) simulation
engine. They can be accessed using the following accessor functions:
Load the GOMC benzene dataset. |
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.
GOMC: Benzene in water
Hydration free energy of benzene using the TraPPE-EH [Raj2007] model and the SPC water model.
Notes
- Data Set Characteristics:
- Number of Legs:
2 (Coulomb, VDW)
- Number of Windows:
7 for Coulomb, 15 for VDW
- Length of Windows:
50 million Monte Carlo steps
- System Size:
1001 molecules
- Temperature:
298 K
- Pressure:
1 bar
- Alchemical Pathway:
vacuum –> vdw –> vdw + coul
- Experimental Hydration Free Energy:
-0.90 ± 0.2 kcal/mol
- Missing Values:
None
- Energy unit:
kJ/mol
- Time unit:
Monte Carlo steps
- Creator:
M. Soroush Barhaghi
- Donor:
Mohammad Soroush Barhaghi (m.soroush@wayne.edu)
- Date:
July 2019
- License:
CC0 Public Domain Dedication
This dataset was generated using GOMC Monte Carlo simulation engine.
Experimental value sourced from [Mobley2013b].
Mobley, David L. (2013). Experimental and Calculated Small Molecule Hydration Free Energies. UC Irvine: Department of Pharmaceutical Sciences, UCI. Retrieved from: https://escholarship.org/uc/item/6sd403pz
Neeraj Rai and J. Ilja Siepmann (2007). The Journal of Physical Chemistry B, 111 (36), 10790-10799 DOI: 10.1021/jp073586l