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