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 the Gromacs benzene dataset. |
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Load the Gromacs ABFE dataset. |
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Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 1 (single simulation visits all states). |
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Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 2 (two simulations visit all states independently). |
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Load the Gromacs Host CB7 Guest C3 REX dataset, case 3. |
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Load the Gromacs water particle with total energy dataset. |
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Load the Gromacs water particle with potential energy dataset. |
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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].
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
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.
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.
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:
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.
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.
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:
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.
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.
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()[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:
- 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:
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].
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