Gromacs datasets

Gromacs molecular dynamics simulation datasets.

The alchemlyb.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_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()

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()

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()

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()

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

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()

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()

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()

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