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imatinib.pdb was generated by running `obabel -imol2 imatinib.mol2 -opdb > imatinib.pdb`
freesolve_v0.3.tar.bz2 is a modified version of David Mobley's FreeSolve database (http://www.escholarship.org/uc/item/6sd403pz). I have deleted the gromacs top files and SDF files to save space in our repo.
1am7_protein.pdb, 1am7_corrected.xtc, and 1am7_uncorrected.xtc are Gromacs trajectories of lambda phage lysozyme (PDB: 1AM7). The uncorrected xtc file has the protein drifting across the periodic box. The
corrected xtc file has been corrected with trjconv -pbc mol. This are useful as a sanity check for PBC issues.
`inpcrd` is an AMBER restart/inpcrd file for a solvated alanine dipeptide. It
was taken from the AmberTools test suite found in `$AMBERHOME/test/netcdf/`.
`ncinpcrd.rst7` is an AMBER NetCDF restart/inpcrd file for the same system as
`inpcrd` (see above)
The following files contain 20 ns (400 frames) of TIP3P water at 300K, 1 atm, simulated using Gromacs 5.0.4. Used for testing thermodynamic property calculation.
See test_thermodynamic_properties.py for details.
tip3p_300K_1ATM.xtc # Trajectory
tip3p_300K_1ATM.pdb # First Frame
md.mdp # A template gromacs mdp file for equilibration and production runs
`well-mixed.hoomdxml` is a HOOMD-Blue XML file of a a coarse-grained free fatty acid +
cholesterol + water system containing 200 free fatty acid and 200 cholesterol chains.
`test_hoomdxml.dcd` is 21 frames of an MD trajectory of the system in `well-mixed.hoomdxml`
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