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].
- 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
- Raj2007
Neeraj Rai and J. Ilja Siepmann (2007). The Journal of Physical Chemistry B, 111 (36), 10790-10799 DOI: 10.1021/jp073586l