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).

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.

alchemtest.namd.load_idws()

Load the NAMD IDWS 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 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.

alchemtest.namd.load_restarted()

Load the NAMD IDWS 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 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:

Bunch