System specifications

Version 0.5

This should be enough to define the end states of the calculation. It should consist in the specific input files for a standard molecular simulation package. The specific files required will depend on the software used:

• GROMACS: a .gro file and a .top file
• AMBER: a .ptrtop file and a .crd file
• DESMOND: a .cms file
• CHARMM: a .crd or .psd file
• LAMMPS: potential file and .txt coordinate input file

Systems specifications require the same force field. Thus, to test different force fields, separate related system specifications are required. Ideally, they would share the same coordinates, but that might not be possible if one was looking at changes in protonation state, etc.

System specifications should also contain a README.txt file which provides information on how the files were generated from raw input.

The system specification should include two sets of coordinate files: complex and solute files. The topologies could be provides as two independent files, or some combination of files (for example, in GROMACS, one can #include files, so the two different .top files could consist almost entirely of #includes of the same ligand and complex files). The key point is both the initial coordinates and all molecular simulation parameters for both calculations are provided.

Velocities may be included, but shouldn't matter. Preference to have them not included (I'm not sure if this is possible for all codes) to avoid clutter than is not directly relevant.

Solvent molecules can either be included or not included. If not included, it is assumed that is only to be used for implicit solvent calculations.

Files should be equilibrated at the experimental temperature and 1 atm. However, it's fine if they are equilibrated at any nearby temperature at 1 atm; as long as they can run without any additional minimization or equilibration at experimental conditions without crashing.

We will eventually want to have all tests cases in a number of file formats. However, the lack of having the same input files should not limit benchmark sets being contributed. Conversion can be performed manually or semimanually (using acepype, etc.) It may be necessary to provide more digits of precision in parameters or configurations to make it possible to convert between simulations.

System specifications from the same molecular system but including different variations--for example, with different protonation states, salt concentrations, etc., will be grouped together.