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. |
|
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.
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).
Notes¶
- Data Set Characteristics:
- Number of Legs
1 (forward mutation in water with IDWS sampling)
- Number of Windows
11
- Length of Windows
50 ps (each window interspersed with 5 ps equilibration)
- System Size
1030 atoms
- Temperature
300 K
- Pressure
1 bar
- Alchemical Pathway
dummy mutation of ethane into ethane using dual topology hybrid molecule. Nonbonded interactions of perturbed atoms are scaled with their environment.
- Theoretical Free Energy difference
0
- Missing Values
None
- Energy unit
kcal/mol
- Time unit
step
- Date
May 2021
- Donor
J Hénin
- License
CC0 Public Domain Dedication
This dataset was generated using the NAMD molecular dynamics engine.
NAMD: free energy of tyrosine to alanine in vacuo¶
Free energy change from mutating a Tyr into Ala in vacuo. Uses Interleaved Double-Wide Sampling (Hénin and Brannigan). Each lambda window was run separately, and NAMD was interrupted and restarted multiple times, such that one window may span multiple fepout files.
Derived from NAMD FEP Tutorial, available at: https://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/
Notes¶
- Data Set Characteristics:
- Number of Legs
1 (forward mutation with IDWS sampling)
- Number of Windows
11
- Length of Windows
50 ps
- System Size
57 atoms
- Temperature
300 K
- Alchemical Pathway
Mutation of Tyr into Ala using hybrid molecule. Nonbonded interactions of perturbed atoms are scaled with their environment.
- Missing Values
None
- Energy unit
kcal/mol
- Time unit
step
- Date
August 2021
- Donor
Thomas T. Joseph
- License
CC0 Public Domain Dedication
This dataset was generated using the NAMD molecular dynamics engine.
NAMD: free energy of tyrosine to alanine in vacuo¶
Free energy change from mutating a Tyr into Ala in vacuo. Uses Interleaved Double-Wide Sampling (Hénin and Brannigan). Each lambda window was run separately, and NAMD was interrupted and restarted multiple times, such that one window may span multiple fepout files.
Derived from NAMD FEP Tutorial, available at: https://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/
This calculation was run from lambda = 1.0 to lambda = 0.0, because it is possible for an IDWS calculation in NAMD to be run this way.
Notes¶
- Data Set Characteristics:
- Number of Legs
1 (forward mutation with IDWS sampling)
- Number of Windows
11
- Length of Windows
50 ps
- System Size
57 atoms
- Temperature
300 K
- Alchemical Pathway
Mutation of Tyr into Ala using hybrid molecule. Nonbonded interactions of perturbed atoms are scaled with their environment.
- Missing Values
None
- Energy unit
kcal/mol
- Time unit
step
- Date
September 2021
- Donor
Thomas T. Joseph
- License
CC0 Public Domain Dedication
This dataset was generated using the NAMD molecular dynamics engine.
-
alchemtest.namd.load_restarted_reversed()¶ Load the NAMD IDWS dataset, run from lambda = 1 -> 0, with interruptions and restarts.
- 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