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. |
|
Load the Gromacs ABFE dataset. |
|
Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 1 (single simulation visits all states). |
|
Load the Gromacs Host CB7 Guest C3 expanded ensemble dataset, case 2 (two simulations visit all states independently). |
|
Load the Gromacs Host CB7 Guest C3 REX dataset, case 3. |
|
Load the Gromacs water particle with total energy dataset. |
|
Load the Gromacs water particle with potential energy dataset. |
|
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
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 This unpublished data uses Host CB7 and Guest C3 from [Muddana2014a].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
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
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
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
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
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
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
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].
- 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
-
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
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