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Molecular dynamics (MD) simulation data for a three-component system [DPPC-DOPC-CHOL]
This dataset contains one file with molecular dynamics (MD) simulation data for a three-component system [DPPC-DOPC-CHOL]. It is the default dataset (3k disordered) used for the P2B1 benchmark. It is a 10 microsecond (μs), coarse-grained bead simulation in Protein Data Bank format containing 3,000 lipids and 3,000 frames. Extracting this 2.87 GB file (3k_run10_10us.35fs-DPPC.10-DOPC.70-CHOL.20.dir.tar.gz) produces a directory called 3k_run10_10us.35fs-DPPC.10-DOPC.70-CHOL.20.dir that contains 29 .npz files, which are the MD simulation data, split into 29 chunks. The first 28 files are 107 MB each; the last is 66 MB. The chunk shape is (100, 3040, 12, 20), the last three dimensions of which correspond to the number of molecules, the number of beads, and the number of features. The data format is [Frames (2900), Molecules (3040), Beads (12), [rel_x, rel_y, rel_z, CHOL, DPPC, DIPC, Head, Tail, BL1, BL2, BL3, BL4, BL5, BL6, BL7, BL8, BL9, BL10, BL11, BL12] (20)]. This is from the BAASiC ADMIRRAL (formerly known as Pilot 2) dataset produced at LLNL (LLNL-MI-724660), produced under contract DE-AC52-07NA27344, and from 11/28/17. For more information, refer to the GitHub Repository (https://github.com/CBIIT/NCI-DOE-Collab-Pilot2-Autoencoder_MD_Simulation_Data).
Molecular dynamics simulation data of membrane interactions of the globular domain and the hypervariable region of KRAS4b
This dataset contains molecular dynamics simulation data for the "Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior" paper (https://elifesciences.org/articles/47654). For each individual simulation, the MoDaC asset provides a topology file (.gro), a PDB file (.pdb), and a sample trajectory of 1μs.
KRAS4b molecular simulation data constructed by the automated system construction in MuMMI.
This dataset contains Multiscale Machine-Learned Modeling Infrastructure (MUMMI) Splash Run 2 simulations for Campaign 1. This dataset contains about 2,089,718 uncompressed files, totaling about 145 TB. The counts represent the files in a state that is approximate of the state found during a simulation campaign. The dataset contains simulation data with the following types of patch tarballs:
|
xtc.tar.gz |
A tarball that contains the system .tpr file and associated .xtc trajectory file. |
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ddcmd.tar.gz |
A tarball containing all ddcMD inputs used in the simulation, .itp parameter files, snapshots to restart the simulation, and analysis/position data. |
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createsims.tar.gz |
A tarball of the system (including intermediate files) as it was constructed by the automated system construction in MuMMI. |
This dataset also contains a macro file (macro.tar.gz).
KRAS4b coarse grained simulation data constructed by the automated system construction in MuMMI along with macro-scale input files and data for simulation
This dataset contains Multiscale Machine-Learned Modeling Infrastructure (MuMMI) Splash Run 4 simulations for Campaign 1. This dataset contains about 6,360,365 uncompressed files, totaling about 212 TB. The counts represent the files in a state that is approximate of the state found during a simulation campaign. The coarse-grained simulation data contains the following types of patch tarballs:
|
xtc.tar.gz |
A tarball that contains the system .tpr file and associated .xtc trajectory file. |
|
ddcmd.tar.gz |
A tarball containing all ddcMD inputs used in the simulation, .itp parameter files, snapshots to restart the simulation, and analysis/position data. |
|
createsims.tar.gz |
A tarball of the system (including intermediate files) as it was constructed by the automated system construction in MuMMI. |
This dataset also contains the following macro-scale input files:
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Macro file and feedback data |
macro.tar.gz |
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Machine learning files |
ml/ |
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Macro-patch data |
pfpatches/ |
RAS-RAF molecular simulation data constructed by the automated system construction in MuMMI.
This dataset contains Multiscale Machine-Learned Modeling Infrastructure (MuMMI) Splash Run simulations for Campaign 3. This dataset contains about 46,380,836 uncompressed files, totaling about 271 TB. The counts represent the files in a state that is approximate of the state found during a simulation campaign. The dataset contains simulation data with the following types of patch tarballs:
|
xtc.tar.gz |
Tarballs that contain the system .tpr file and associated .xtc trajectory file. |
|
ddcmd.tar.gz |
Tarballs containing all ddcMD inputs used in the simulation, .itp parameter files, snapshots to restart the simulation, and analysis/position data. |
|
createsims.tar.gz |
Micro-scale input files as it was constructed by the automated system construction in MuMMI. |
|
backmapping.tar.gz |
All-Atomistic (AA) input files and data |
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amber.tar.gz |
AMBER simulation and analysis files |
This dataset also contains folders for macro, ml, and patches.
Collection of parameters and inputs files for running molecular dynamics computer simulations of RAS proteins associated with a lipid-based cell membrane model in water, as well as resulting time-trajectories of atomic motion in these simulations
This dataset contains 6,401 files that describe parameters and other inputs for running molecular dynamics computer simulations of RAS proteins associated with a lipid-based cell membrane model in water, as well as resulting time-trajectories of atomic motion in these simulations. Specifically, this dataset includes:
- Twenty-one (21) files containing generalized force field parameters.
- Twenty-two (22) files of similar format and content for each of 290 separate molecular dynamics simulations (22 * 290 = 6,380).
The total size of this dataset is 1.0 TB.