Gromacs datasets

Gromacs molecular dynamics simulation datasets.

The alchemlyb.gmx module features datasets generated using the Gromacs molecular dynamics engine. They can be accessed using the following accessor functions:

load_benzene()

Load the Gromacs benzene dataset.

Gromacs: Benzene in water

Notes

Data Set Characteristics:

Number of Legs:2 (Coulomb, VDW) Number of Windows:  5 for Coulomb, 16 for VDW Length of Windows:  40ns 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 Creator:I. Kenney Donor:Ian Kenney (ian.kenney@asu.edu) Date:March 2017

Benzene in water, alchemically turned into benzene in vacuum separated from water

This dataset was generated using MDPOW, with the Gromacs molecular dynamics engine.

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.gmx.load_benzene()

Load the Gromacs benzene dataset.

Returns:data – Dictionary-like object, the interesting attributes are: - ‘data’ : the data files by alchemical leg - ‘DESCR’: the full description of the dataset Return type:Bunch