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 the NAMD tyrosine to alanine mutation 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.