NAMD datasets¶

NAMD molecular dynamics simulation datasets.

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

`load_tyr2ala`()	Load the NAMD tyrosine to alanine mutation dataset.
`load_idws`()	Load the NAMD IDWS dataset.

NAMD: free energy of tyrosine to alanine mutation in aqueous solution¶

Free energy change from mutating a tyrosine (Y) residue into alanine (A) in the Ala-Tyr-Ala tripeptide in aqueous environment.

Notes¶

Data Set Characteristics:

Number of Legs: 2 (forward Y–>A, backward A–>Y)
Number of Windows: 20 for each leg
Length of Windows: 1000 ps (each window interspersed with 200 ps equilibration)
System Size: 1521 atoms
Temperature: 300 K
Pressure: 1 bar
Alchemical Pathway: Point mutation of Tyr to Ala using dual topology hybrid molecule. Nonbonded interactions of perturbed atoms are scaled with their environment.
Experimental Free Energy difference: N/A
Missing Values: None
Energy unit: kcal/mol
Time unit: step
Date: Oct 2017
Donor: JC Gumbart
License: CC0 Public Domain Dedication

This dataset was generated using the NAMD molecular dynamics engine.

alchemtest.namd.load_tyr2ala()¶

Load the NAMD tyrosine to alanine mutation 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

NAMD: free energy of dummy ethane to ethane “mutation” in aqueous solution¶

Free energy change from mutating an ethane molecule into an ethane molecule, turning a H atom into a methyl group and conversely. Expected free energy is zero, however the dataset is tiny (sufficient for testing purposes). Uses Interleaved Double-Wide Sampling (Hénin and Brannigan).