Gromacs datasets

Gromacs molecular dynamics simulation datasets.

The alchemtest.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.

load_ABFE()

Load the Gromacs ABFE dataset.

load_expanded_ensemble_case_1()

Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 1 (single simulation visits all states).

load_expanded_ensemble_case_2()

Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 2 (two simulations visit all states independently).

load_expanded_ensemble_case_3()

Load the Gromacs Host CB7 Guest C3 REX dataset, case 3.

load_water_particle_with_total_energy()

Load the Gromacs water particle with total energy dataset.

load_water_particle_with_potential_energy()

Load the Gromacs water particle with potential energy dataset.

load_water_particle_without_energy()

Load the Gromacs water particle without energy dataset.

Simple TI and FEP

The data sets contain derivatives of the Hamiltonian (TI) and free energy perturbation (FEP) data suitable for processing with FEP estimators as well as BAR/MBAR. Individual \(\lambda\) windows were run independently.

Gromacs: Benzene in water

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

Energy unit:

kJ/mol

Time unit:

ps

Creator:

I. Kenney

Donor:

Ian Kenney (ian.kenney@asu.edu)

Date:

March 2017

License:

CC0 Public Domain Dedication

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()[source]

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

Extended ensemble

Data for extended ensemble simulations; case 1 and case 2 are extended ensembles in the alchemical parameters, case 3 includes replica exchange (REX).

Gromacs: Host CB7 and Guest C3 in water

Host CB7 and Guest C3 in water, Guest C3 alchemically turned into Guest C3 in vacuum separated from water and Host CB7. This unpublished data uses Host CB7 and Guest C3 from [Muddana2014a]. Similar published data can be found in [Monroe2014a].

Notes

Data Set Characteristics:
Number of Legs:

2 (Coulomb, VDW)

Number of Windows:

32 total, 20 for Coulomb, 12 for VDW

Number of Simulations:

1

Length of Simulation:

100ns

System Size:

8286 atoms

Temperature:

300 K

Alchemical Pathway:

vdw + coul –> vdw –> vacuum

Missing Values:

None

Energy unit:

kJ/mol

Time unit:

ps

Creator:

T. Jensen

Donor:

Travis Jensen (travis.jensen@colorado.edu)

Date:

November 2017

License:

CC0 Public Domain Dedication

This dataset was generated using the expanded ensemble algorithm in the Gromacs molecular dynamics engine.

[Muddana2014a]

  1. Muddana, A. Fenley, D. Mobley, and M. Gilson. The SAMPL4 host–guest blind prediction challenge: an overview. Journal of Computer-Aided Molecular Design, 28(4):305–317, 2014. PMID: 24599514. DOI: 10.1007/s10822-014-9735-1.

[Monroe2014a]

  1. Monroe and M. Shirts. Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations. Journal of Computer-Aided Molecular Design, 28(4):401–415, 2014. PMID: 24610238 DOI: 10.1007/s10822-014-9716-4.

alchemtest.gmx.load_expanded_ensemble_case_1()[source]

Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 1 (single simulation visits all states).

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

Gromacs: Host CB7 and Guest C3 in water

Host CB7 and Guest C3 in water, Guest C3 alchemically turned into Guest C3 in vacuum separated from water and Host CB7. This unpublished data uses Host CB7 and Guest C3 from [Muddana2014b]. Similar published data can be found in [Monroe2014b].

Notes

Data Set Characteristics:
Number of Legs:

2 (Coulomb, VDW)

Number of Windows:

32 total, 20 for Coulomb, 12 for VDW

Number of Simulations:

2

Length of Simulation:

50ns

System Size:

8286 atoms

Temperature:

300 K

Alchemical Pathway:

vdw + coul –> vdw –> vacuum

Missing Values:

None

Energy unit:

kJ/mol

Time unit:

ps

Creator:

T. Jensen

Donor:

Travis Jensen (travis.jensen@colorado.edu)

Date:

November 2017

License:

CC0 Public Domain Dedication

This dataset was generated using the expanded ensemble algorithm in the Gromacs molecular dynamics engine.

[Muddana2014b]

  1. Muddana, A. Fenley, D. Mobley, and M. Gilson. The SAMPL4 host–guest blind prediction challenge: an overview. Journal of Computer-Aided Molecular Design, 28(4):305–317, 2014. PMID: 24599514. DOI: 10.1007/s10822-014-9735-1.

[Monroe2014b]

  1. Monroe and M. Shirts. Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations. Journal of Computer-Aided Molecular Design, 28(4):401–415, 2014. PMID: 24610238 DOI: 10.1007/s10822-014-9716-4.

alchemtest.gmx.load_expanded_ensemble_case_2()[source]

Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 2 (two simulations visit all states independently).

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

Gromacs: Host CB7 and Guest C3 in water

Host CB7 and Guest C3 in water, Guest C3 alchemically turned into Guest C3 in vacuum separated from water and Host CB7. This unpublished data uses Host CB7 and Guest C3 from [Muddana2014c].

Notes

Data Set Characteristics:
Number of Legs:

2 (Coulomb, VDW)

Number of Windows:

32 total, 20 for Coulomb, 12 for VDW

Number of Simulations:

32

Length of Simulation:

5ns

System Size:

8286 atoms

Temperature:

300 K

Alchemical Pathway:

vdw + coul –> vdw –> vacuum

Missing Values:

None

Energy unit:

kJ/mol

Time unit:

ps

Creator:

T. Jensen

Donor:

Travis Jensen (travis.jensen@colorado.edu)

Date:

November 2017

License:

CC0 Public Domain Dedication

This dataset was generated using the REX algorithm in the Gromacs molecular dynamics engine.

[Muddana2014c]

  1. Muddana, A. Fenley, D. Mobley, and M. Gilson. The SAMPL4 host–guest blind prediction challenge: an overview. Journal of Computer-Aided Molecular Design, 28(4):305–317, 2014. PMID: 24599514. DOI: 10.1007/s10822-014-9735-1.

alchemtest.gmx.load_expanded_ensemble_case_3()[source]

Load the Gromacs Host CB7 Guest C3 REX dataset, case 3.

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

Water particle TI and FEP

3 simple dH/dl and U_nk datasets of a single water particle from a simulations of water between to hydrophilic surfaces. One dataset contains a total energy column, one contains a potential energy column and one does not contain a energy column.

Gromacs: water particle

Free energy estimation of a water particle between to hydrophilic surfaces

Notes

Data Set Characteristics:
Number of Legs:

2 (Coulomb, VDW)

Number of Windows:

17 for Coulomb, 20 for VDW

Length of Windows:

10ns

System Size:

3312 atoms

Temperature:

300 K

Ensemble:

NVT

Volume:

70.204 nm^3

Alchemical Pathway:

vacuum –> vdw –> vdw + coul

Missing Values:

None

Creator:

D. Wille

Donor:

Dominik Wille (harlor@web.de)

Date:

November 2018

License:

CC0 Public Domain Dedication

Similar free energy estimations can be found in [Schlaich2017].

[Schlaich2017]

Alexander Schlaich, Julian Kappler, and Roland R. Netz. Hydration Friction in Nanoconfinement: From Bulk via Interfacial to Dry Friction. Nano Lett., 2017, 17 (10), pp 5969–5976. DOI: 10.1021/acs.nanolett.7b02000.

alchemtest.gmx.load_water_particle_with_total_energy()[source]

Load the Gromacs water particle with total energy 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

alchemtest.gmx.load_water_particle_with_potential_energy()[source]

Load the Gromacs water particle with potential energy 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

alchemtest.gmx.load_water_particle_without_energy()[source]

Load the Gromacs water particle without energy 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

Absolute Binding Free Energy of n-phenylglycinonitrile to T4 lysozyme

The dataset for computing the absolute binding free energy of n-phenylglycinonitrile to T4 lysozyme. The calculation has two legs: complex and ligand. In the complex leg, restraint is applied to the ligand and the coulombic as well as the Van der Waals interactions are decoupled sequentially. In the ligand leg, only the coulombic and Van der Waals interactions are decoupled.

Gromacs: n-phenylglycinonitrile in T4 lysozyme

Obtain the absolute binding free energy of the n-phenylglycinonitrile for T4 lysozyme by alchemically turning n-phenylglycinonitrile in T4 lysozyme and water into vacuum.

Notes

Data Set Characteristics:
Number of Legs:

2 (Restraint, Coulomb, VDW for protein; Coulomb, VDW for water)

Number of Windows:

11 for Restraint, 5 for Coulomb, 16 for VDW

Length of Windows:

1ns for protein and 5ns for water

System Size:

33005 atoms for protein and 2103 atoms for water

Temperature:

300 K

Pressure:

1 bar

Alchemical Pathway:

vdw + coul –> restraint + vdw + coul –> restraint + vdw –> restraint + vacuum

Reference Hydration Free Energy in protein:

-21.721 +- 0.089 kcal/mol

Reference Hydration Free Energy in water:

-7.679 +- 0.080 kcal/mol

Missing Values:

None

Energy unit:

kJ/mol

Time unit:

ps

Creator:

Z. Wu

Donor:

Zhiyi Wu (zhiyi.wu@bioch.ox.ac.uk)

Date:

March 2021

License:

CC0 Public Domain Dedication

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

Data sourced from [Boyce2009].

[Boyce2009]

Boyce, S.E., Mobley, D.L., Rocklin, G.J., Graves, A.P., Dill, K.A., Shoichet, B.K. (2009) Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site. J. Mol. Biol. 394, 747–7636

alchemtest.gmx.load_ABFE()[source]

Load the Gromacs ABFE 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