| __init__(self, name="gmx", kwargs) | src.gmxio.GMX | |
| AtomLists | src.gmxio.GMX | |
| AtomMask | src.gmxio.GMX | |
| calc_scd(self, n_snap, timestep) | src.gmxio.GMX | |
| callgmx(self, command, stdin=None, print_to_screen=False, print_command=False, kwargs) | src.gmxio.GMX | |
| double | src.gmxio.GMX | |
| energy(self, traj=None) | src.gmxio.GMX | |
| energy_dipole(self, traj=None) | src.gmxio.GMX | |
| energy_force(self, force=True, traj=None) | src.gmxio.GMX | |
| energy_force_one(self, shot) | src.gmxio.GMX | |
| energy_one(self, shot) | src.gmxio.GMX | |
| energy_rmsd(self, shot, optimize=True) | src.gmxio.GMX | |
| energy_termnames(self, edrfile=None) | src.gmxio.GMX | |
| evaluate_(self, force=False, dipole=False, traj=None) | src.gmxio.GMX | |
| evaluate_snapshot(self, shot, force=False, dipole=False) | src.gmxio.GMX | |
| evaluate_trajectory(self, force=False, dipole=False, traj=None) | src.gmxio.GMX | |
| generate_positions(self) | src.gmxio.GMX | |
| get_charges(self) | src.gmxio.GMX | |
| gmx_defs | src.gmxio.GMX | |
| gmx_eq_barostat | src.gmxio.GMX | |
| gmxpath | src.gmxio.GMX | |
| gmxsuffix | src.gmxio.GMX | |
| gmxversion | src.gmxio.GMX | |
| have_constraints | src.gmxio.GMX | |
| interaction_energy(self, fraga, fragb) | src.gmxio.GMX | |
| links(self) | src.gmxio.GMX | |
| make_gro_trajectory(self, fout=None) | src.gmxio.GMX | |
| md(self, nsteps=0, nequil=0, verbose=False, deffnm=None, kwargs) | src.gmxio.GMX | |
| mdene | src.gmxio.GMX | |
| mdp | src.gmxio.GMX | |
| mdtraj | src.gmxio.GMX | |
| mol | src.gmxio.GMX | |
| molecular_dynamics(self, nsteps, timestep, temperature=None, pressure=None, nequil=0, nsave=0, minimize=True, threads=None, verbose=False, bilayer=False, kwargs) | src.gmxio.GMX | |
| multipole_moments(self, shot=0, optimize=True, polarizability=False) | src.gmxio.GMX | |
| n_nonwater(self, structure_file) | src.gmxio.GMX | |
| n_snaps(self, nsteps, step_interval, timestep) | src.gmxio.GMX | |
| normal_modes(self, shot=0, optimize=True) | src.gmxio.GMX | |
| optimize(self, shot, crit=1e-4, align=True, kwargs) | src.gmxio.GMX | |
| pbc | src.gmxio.GMX | |
| prepare(self, pbc=False, kwargs) | src.gmxio.GMX | |
| readsrc(self, kwargs) | src.gmxio.GMX | |
| scd_persnap(self, ndx, timestep, final_frame) | src.gmxio.GMX | |
| setopts(self, kwargs) | src.gmxio.GMX | |
| top | src.gmxio.GMX | |
| valkwd | src.gmxio.GMX | |
| warngmx(self, command, warnings=[], maxwarn=1, kwargs) | src.gmxio.GMX | |
1.8.13