Index

A

add_angle() (mstk.topology.Molecule method) add_atom() (mstk.topology.Molecule method) add_bond() (mstk.topology.Molecule method) add_dihedral() (mstk.topology.Molecule method) add_improper() (mstk.topology.Molecule method) add_parameter() (mstk.forcefield.PeriodicDihedralTerm method) add_residue() (mstk.topology.Molecule method) add_term() (mstk.forcefield.ForceField method) all_jobs (mstk.scheduler.Scheduler property) alpha (mstk.forcefield.DrudeTerm attribute) (mstk.topology.Atom attribute) Angle (class in mstk.topology) angle_classes (mstk.simsys.System attribute) angle_terms (mstk.forcefield.ForceField attribute) (mstk.simsys.System attribute) angles (mstk.topology.Dihedral property) (mstk.topology.Molecule property) (mstk.topology.Topology property) (mstk.topology.UnitCell property) AngleTerm (class in mstk.forcefield) assign_charge() (mstk.forcefield.ForceField method) assign_mass() (mstk.forcefield.ForceField method) Atom (class in mstk.topology) atom1 (mstk.topology.Angle attribute) (mstk.topology.Bond attribute) (mstk.topology.Dihedral attribute) (mstk.topology.Improper attribute)

atom2 (mstk.topology.Angle attribute) (mstk.topology.Bond attribute) (mstk.topology.Dihedral attribute) (mstk.topology.Improper attribute) atom3 (mstk.topology.Angle attribute) (mstk.topology.Dihedral attribute) (mstk.topology.Improper attribute) atom4 (mstk.topology.Dihedral attribute) (mstk.topology.Improper attribute) atom_types (mstk.forcefield.ForceField attribute) atoms (mstk.chem.formula.Formula attribute) (mstk.topology.Angle property) (mstk.topology.Bond property) (mstk.topology.Dihedral property) (mstk.topology.Improper property) (mstk.topology.Molecule property) (mstk.topology.Residue property) (mstk.topology.Topology property) AtomType (class in mstk.forcefield) attraction (mstk.forcefield.MieTerm attribute) average_of_blocks() (in module mstk.analyzer.series)

B

block_average() (in module mstk.analyzer.series) Bond (class in mstk.topology) Bond.Order (class in mstk.topology) bond_classes (mstk.simsys.System attribute) bond_partners (mstk.topology.Atom property) bond_terms (mstk.forcefield.ForceField attribute) (mstk.simsys.System attribute)

bonds (mstk.topology.Angle property) (mstk.topology.Atom property) (mstk.topology.Dihedral property) (mstk.topology.Molecule property) (mstk.topology.Topology property) BondTerm (class in mstk.forcefield) build_box() (mstk.wrapper.Packmol method)

C

cached_jobs_expire (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute) calc_a_k_linear() (mstk.forcefield.LinearAngleTerm method) calc_com() (in module mstk.analyzer.structure) calc_hull_volume() (in module mstk.analyzer.structure) calc_lengths_angles_from_vectors() (mstk.topology.UnitCell static method) calc_position() (mstk.topology.TIP4PSite method) (mstk.topology.VirtualSite method) calc_rg() (in module mstk.analyzer.structure) calc_vectors_from_lengths_angles() (mstk.topology.UnitCell static method) calc_weighted_average() (in module mstk.analyzer.structure) cell (mstk.topology.Topology attribute) (mstk.trajectory.Frame attribute) charge (mstk.forcefield.AtomType attribute) (mstk.topology.Atom attribute) charged (mstk.simsys.System attribute) ChargeIncrementTerm (class in mstk.forcefield)

charges (mstk.trajectory.Frame attribute) check_vle_density() (in module mstk.analyzer.vle) CheckpointReporter (class in mstk.ommhelper.reporter) close() (mstk.trajectory.CombinedTrj method) (mstk.trajectory.Dcd method) (mstk.trajectory.Trajectory method) (mstk.trajectory.TrjHandler method) (mstk.trajectory.Xtc method) CLPolCoulTT() (in module mstk.ommhelper.force) CombinedTrj (class in mstk.trajectory) comments (mstk.forcefield.FFTerm attribute) constrain_angles (mstk.simsys.System attribute) constrain_bonds (mstk.simsys.System attribute) create() (mstk.topology.VirtualSite static method) create_from_zff() (mstk.forcefield.FFTermFactory static method) create_from_zfp() (mstk.forcefield.FFTermFactory static method) create_mol_from_smiles() (in module mstk.chem.rdkit) curve_fit_rsq() (in module mstk.analyzer.fitting)

D

d (mstk.forcefield.TIP4PSiteTerm attribute) Dcd (class in mstk.trajectory) decompose_energy() (mstk.simsys.System method) density() (mstk.wrapper.GMX method) depth (mstk.forcefield.MorseBondTerm attribute) describeNextReport() (mstk.ommhelper.reporter.CheckpointReporter method) (mstk.ommhelper.reporter.DrudeTemperatureReporter method) (mstk.ommhelper.reporter.GroReporter method) (mstk.ommhelper.reporter.StateDataReporter method) (mstk.ommhelper.reporter.ViscosityReporter method) diffusion() (mstk.wrapper.GMX method) Dihedral (class in mstk.topology)

dihedral_classes (mstk.simsys.System attribute) dihedral_terms (mstk.forcefield.ForceField attribute) (mstk.simsys.System attribute) dihedrals (mstk.topology.Molecule property) (mstk.topology.Topology property) DihedralTerm (class in mstk.forcefield) DONE (mstk.scheduler.PbsJob.State attribute) DOUBLE (mstk.topology.Bond.Order attribute) download() (mstk.scheduler.RemoteSlurm method) (mstk.scheduler.Scheduler method) drude_pairs (mstk.simsys.System attribute) DrudeTemperatureReporter (class in mstk.ommhelper.reporter) DrudeTerm (class in mstk.forcefield)

E

efficiency_with_block_size() (in module mstk.analyzer.series) electric_field() (in module mstk.ommhelper.force) Element (class in mstk.chem.element) energy() (mstk.wrapper.GMX method) env_cmd (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute) epsilon (mstk.forcefield.LJ126Term attribute) (mstk.forcefield.MieTerm attribute) eqt_ang_c (mstk.forcefield.AtomType attribute) eqt_ang_s (mstk.forcefield.AtomType attribute) eqt_bond (mstk.forcefield.AtomType attribute) eqt_dih_c (mstk.forcefield.AtomType attribute) eqt_dih_s (mstk.forcefield.AtomType attribute) eqt_imp_c (mstk.forcefield.AtomType attribute) eqt_imp_s (mstk.forcefield.AtomType attribute) eqt_polar (mstk.forcefield.AtomType attribute) eqt_q_inc (mstk.forcefield.AtomType attribute) eqt_types (mstk.forcefield.AtomType property) eqt_vdw (mstk.forcefield.AtomType attribute) equals() (mstk.topology.Angle method) (mstk.topology.Bond method) (mstk.topology.Dihedral method) (mstk.topology.Improper method)

evaluate() (mstk.topology.Angle method) (mstk.topology.Bond method) (mstk.topology.Dihedral method) (mstk.topology.Improper method) evaluate_energy() (mstk.forcefield.FFTerm method) (mstk.forcefield.HarmonicAngleTerm method) (mstk.forcefield.HarmonicBondTerm method) (mstk.forcefield.HarmonicImproperTerm method) (mstk.forcefield.LJ126Term method) (mstk.forcefield.MieTerm method) (mstk.forcefield.MorseBondTerm method) (mstk.forcefield.OplsDihedralTerm method) (mstk.forcefield.OplsImproperTerm method) (mstk.forcefield.PeriodicDihedralTerm method) exclude (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Slurm attribute) export() (mstk.simsys.GromacsExporter static method) (mstk.simsys.LammpsExporter static method) (mstk.simsys.NamdExporter static method) (mstk.simsys.OpenMMExporter static method) export_gromacs() (mstk.simsys.System method) export_lammps() (mstk.simsys.System method) export_namd() (mstk.simsys.System method) extend_tpr() (mstk.wrapper.GMX method)

F

factor_energy() (mstk.forcefield.MieTerm method) factor_r_min() (mstk.forcefield.MieTerm method) ff (mstk.simsys.System property) ff_classes (mstk.simsys.System attribute) FFTerm (class in mstk.forcefield) FFTermFactory (class in mstk.forcefield) fit_vle_dminus() (in module mstk.analyzer.fitting) fit_vle_dplus() (in module mstk.analyzer.fitting) fixed (mstk.forcefield.AngleTerm attribute) (mstk.forcefield.BondTerm attribute) (mstk.forcefield.HarmonicAngleTerm attribute) (mstk.forcefield.HarmonicBondTerm attribute) (mstk.forcefield.LinearAngleTerm attribute) (mstk.forcefield.SDKAngleTerm attribute)

ForceField (class in mstk.forcefield) forcefield (mstk.forcefield.Padua attribute) (mstk.forcefield.Ppf attribute) (mstk.forcefield.Zff attribute) (mstk.forcefield.Zfp attribute) formal_charge (mstk.topology.Atom attribute) Formula (class in mstk.chem.formula) Frame (class in mstk.trajectory) frame (mstk.trajectory.Trajectory attribute) from_rdmol() (mstk.topology.Molecule static method) from_smiles() (mstk.topology.Molecule static method)

G

GaffTyper (class in mstk.forcefield.typer) Gauss (class in mstk.wrapper) gen_inp() (mstk.wrapper.Packmol static method) generate_angle_dihedral_improper() (mstk.topology.Molecule method) (mstk.topology.Topology method) generate_conformers() (mstk.topology.Molecule method) generate_drude_particles() (mstk.topology.Molecule method) (mstk.topology.Topology method) generate_gjf_cv() (mstk.wrapper.Gauss method) generate_gpu_multidir_cmds() (mstk.wrapper.GMX method) generate_sh() (mstk.scheduler.Scheduler method) (mstk.scheduler.Slurm method) generate_top() (mstk.wrapper.GMX static method) generate_top_for_hvap() (mstk.wrapper.GMX static method) generate_virtual_sites() (mstk.topology.Molecule method) (mstk.topology.Topology method) get_12_13_14_pairs() (mstk.topology.Molecule method) (mstk.topology.Topology method) get_adjacency_matrix() (mstk.topology.Molecule method) get_alias() (mstk.forcefield.FFTerm class method) get_all_jobs() (mstk.scheduler.RemoteSlurm method) (mstk.scheduler.Scheduler method) (mstk.scheduler.Slurm method) get_angle_term() (mstk.forcefield.ForceField method) get_bond_term() (mstk.forcefield.ForceField method) get_box() (mstk.wrapper.GMX method) get_charge() (mstk.forcefield.DrudeTerm method) get_dihedral_term() (mstk.forcefield.ForceField method) get_distance_matrix() (mstk.topology.Molecule method) get_drude_pairs() (mstk.topology.Molecule method) (mstk.topology.Topology method) get_eqt_for_angle() (mstk.forcefield.ForceField method) get_eqt_for_bond() (mstk.forcefield.ForceField method) get_eqt_for_dihedral() (mstk.forcefield.ForceField method)

get_eqt_for_improper() (mstk.forcefield.ForceField method) get_eqt_for_qinc() (mstk.forcefield.ForceField method) get_fluct_props() (mstk.wrapper.GMX method) get_handler_for_file() (mstk.trajectory.TrjHandler static method) get_improper_term() (mstk.forcefield.ForceField method) get_info() (mstk.trajectory.CombinedTrj method) (mstk.trajectory.Dcd method) (mstk.trajectory.Gro method) (mstk.trajectory.LammpsTrj method) (mstk.trajectory.TrjHandler method) (mstk.trajectory.Xtc method) (mstk.trajectory.Xyz method) get_job_from_name() (mstk.scheduler.Scheduler method) get_properties_stderr() (mstk.wrapper.GMX method) get_property_stderr() (mstk.wrapper.GMX method) get_qinc_term() (mstk.forcefield.ForceField method) get_settings() (mstk.forcefield.ForceField method) get_sub_molecule() (mstk.topology.Molecule method) get_TIP4P_linear_coeffs() (mstk.simsys.System method) get_top_mol_numbers() (mstk.wrapper.GMX static method) get_unique_molecules() (mstk.topology.Topology method) get_vdw_term() (mstk.forcefield.ForceField method) get_virtual_site_pairs() (mstk.topology.Molecule method) (mstk.topology.Topology method) getBoxSizeAverage() (mstk.ommhelper.reporter.StateDataReporter method) GMX (class in mstk.wrapper) Gro (class in mstk.trajectory) GroFile (class in mstk.ommhelper) GromacsExporter (class in mstk.simsys) grompp() (mstk.wrapper.GMX method) GroReporter (class in mstk.ommhelper.reporter) GroTopology (class in mstk.topology) guess_connectivity_from_ff() (mstk.topology.Molecule method) (mstk.topology.Topology method) guess_from_atom_type() (mstk.chem.element.Element static method)

H

HarmonicAngleTerm (class in mstk.forcefield) HarmonicBondTerm (class in mstk.forcefield) HarmonicImproperTerm (class in mstk.forcefield) has_charge (mstk.trajectory.Frame attribute) has_position (mstk.topology.Atom attribute) (mstk.topology.Molecule property) (mstk.topology.Topology property)

has_velocity (mstk.trajectory.Frame attribute) has_virtual_site (mstk.forcefield.ForceField property) (mstk.topology.Topology property) host (mstk.scheduler.RemoteSlurm attribute)

I

id (mstk.scheduler.PbsJob attribute) (mstk.topology.Atom attribute) (mstk.topology.Molecule attribute) id_in_mol (mstk.topology.Atom attribute) Improper (class in mstk.topology) improper_classes (mstk.simsys.System attribute) improper_terms (mstk.forcefield.ForceField attribute) (mstk.simsys.System attribute) impropers (mstk.topology.Molecule property) (mstk.topology.Topology property) ImproperTerm (class in mstk.forcefield) init_from_omm_topology() (mstk.topology.Topology method) is_aromatic (mstk.topology.Bond property) is_conjugated (mstk.topology.Bond property) is_converged() (in module mstk.analyzer.series) is_drude (mstk.topology.Atom attribute) (mstk.topology.Bond property) (mstk.topology.Topology property)

is_linear (mstk.forcefield.AngleTerm property) (mstk.forcefield.HarmonicAngleTerm property) (mstk.forcefield.LinearAngleTerm property) (mstk.forcefield.SDKAngleTerm property) is_polarizable (mstk.forcefield.ForceField property) is_rectangular (mstk.topology.UnitCell property) is_remote (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute) is_running() (mstk.scheduler.Scheduler method) is_sdk (mstk.forcefield.MieTerm property) is_similar_to() (mstk.topology.Molecule method) is_working() (mstk.scheduler.RemoteSlurm method) (mstk.scheduler.Scheduler method) (mstk.scheduler.Slurm method) is_zero (mstk.forcefield.DihedralTerm property) (mstk.forcefield.OplsDihedralTerm property) (mstk.forcefield.PeriodicDihedralTerm property)

K

k (mstk.forcefield.DrudeTerm attribute) (mstk.forcefield.HarmonicAngleTerm attribute) (mstk.forcefield.HarmonicBondTerm attribute) (mstk.forcefield.HarmonicImproperTerm attribute) (mstk.forcefield.LinearAngleTerm attribute) (mstk.forcefield.MorseBondTerm attribute) (mstk.forcefield.OplsImproperTerm attribute) (mstk.forcefield.SDKAngleTerm attribute)

k1 (mstk.forcefield.OplsDihedralTerm attribute) k2 (mstk.forcefield.OplsDihedralTerm attribute) k3 (mstk.forcefield.OplsDihedralTerm attribute) k4 (mstk.forcefield.OplsDihedralTerm attribute) kill_job() (mstk.scheduler.RemoteSlurm method) (mstk.scheduler.Scheduler method) (mstk.scheduler.Slurm method)

L

LammpsData (class in mstk.topology) LammpsExporter (class in mstk.simsys) LammpsTrj (class in mstk.trajectory) length (mstk.forcefield.BondTerm attribute) (mstk.forcefield.HarmonicBondTerm attribute) (mstk.forcefield.MorseBondTerm attribute) lengths (mstk.topology.UnitCell property)

LinearAngleTerm (class in mstk.forcefield) LJ126Term (class in mstk.forcefield) LJ_MIXING_GEOMETRIC (mstk.forcefield.ForceField attribute) LJ_MIXING_LB (mstk.forcefield.ForceField attribute) LJ_MIXING_NONE (mstk.forcefield.ForceField attribute) lj_mixing_rule (mstk.forcefield.ForceField attribute) (mstk.forcefield.ForceField property)

M

majorversion (mstk.wrapper.GMX attribute) mass (mstk.forcefield.AtomType attribute) (mstk.forcefield.DrudeTerm attribute) (mstk.topology.Atom attribute) max_running_hour (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute) mdrun() (mstk.wrapper.GMX method) merge() (mstk.topology.Molecule static method) merge_alpha_H (mstk.forcefield.DrudeTerm attribute) MieTerm (class in mstk.forcefield) minimize_energy() (mstk.simsys.System method)

modify_lj96() (mstk.wrapper.GMX static method) modify_top_mol_numbers() (mstk.wrapper.GMX static method) module mstk.chem.constant mstk.chem.rdkit Molecule (class in mstk.topology) molecule (mstk.topology.Atom property) molecules (mstk.topology.Topology property) MorseBondTerm (class in mstk.forcefield) mstk.chem.constant module mstk.chem.rdkit module

N

n_angle (mstk.topology.Molecule property) (mstk.topology.Topology property) n_atom (mstk.topology.Molecule property) (mstk.topology.Residue property) (mstk.topology.Topology property) (mstk.trajectory.Trajectory attribute) n_atom_type (mstk.topology.LammpsData attribute) n_bond (mstk.topology.Molecule property) (mstk.topology.Topology property) n_dihedral (mstk.topology.Molecule property) (mstk.topology.Topology property) n_frame (mstk.trajectory.Trajectory attribute) n_gpu (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute) n_h (mstk.chem.formula.Formula property) n_heavy (mstk.chem.formula.Formula property) n_improper (mstk.topology.Molecule property) (mstk.topology.Topology property) n_molecule (mstk.topology.Topology property) n_node (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Slurm attribute) n_proc (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute)

n_residue (mstk.topology.Molecule property) (mstk.topology.Topology property) n_running_jobs (mstk.scheduler.Scheduler property) N_vaporize_condense() (in module mstk.analyzer.vle) NamdExporter (class in mstk.simsys) name (mstk.forcefield.AngleTerm property) (mstk.forcefield.AtomType property) (mstk.forcefield.BondTerm property) (mstk.forcefield.ChargeIncrementTerm property) (mstk.forcefield.DihedralTerm property) (mstk.forcefield.FFTerm property) (mstk.forcefield.ImproperTerm property) (mstk.forcefield.PolarizableTerm property) (mstk.forcefield.VdwTerm property) (mstk.forcefield.VirtualSiteTerm property) (mstk.scheduler.PbsJob attribute) (mstk.topology.Angle property) (mstk.topology.Atom attribute) (mstk.topology.Bond property) (mstk.topology.Dihedral property) (mstk.topology.Improper property) (mstk.topology.Molecule attribute) (mstk.topology.Molecule property)

O

open() (mstk.forcefield.ForceField static method) (mstk.topology.Topology static method) (mstk.trajectory.Trajectory static method) OpenMMExporter (class in mstk.simsys)

OplsDihedralTerm (class in mstk.forcefield) OplsImproperTerm (class in mstk.forcefield) order (mstk.topology.Bond attribute) (mstk.topology.Bond property)

P

Packmol (class in mstk.wrapper) Padua (class in mstk.forcefield) PaduaLJScaler (class in mstk.forcefield) pairwise_vdw_terms (mstk.forcefield.ForceField attribute) parameters (mstk.forcefield.PeriodicDihedralTerm attribute) PbsJob (class in mstk.scheduler) PbsJob.State (class in mstk.scheduler) Pdb (class in mstk.topology) pdb2gro() (mstk.wrapper.GMX method) PENDING (mstk.scheduler.PbsJob.State attribute) PeriodicDihedralTerm (class in mstk.forcefield) PeriodicDihedralTerm.Parameter (class in mstk.forcefield) phi (mstk.forcefield.HarmonicImproperTerm attribute) point_wall_power() (in module mstk.ommhelper.force) polarizable_classes (mstk.simsys.System attribute) polarizable_terms (mstk.forcefield.ForceField attribute) (mstk.simsys.System attribute)

PolarizableTerm (class in mstk.forcefield) polyfit() (in module mstk.analyzer.fitting) polyfit_2d() (in module mstk.analyzer.fitting) polyval() (in module mstk.analyzer.fitting) polyval_derivative() (in module mstk.analyzer.fitting) polyval_derivative_2d() (in module mstk.analyzer.fitting) port (mstk.scheduler.RemoteSlurm attribute) position (mstk.topology.Atom property) positions (mstk.topology.Molecule property) (mstk.topology.Topology property) (mstk.trajectory.Frame attribute) Ppf (class in mstk.forcefield) predict_scale_epsilon() (mstk.forcefield.PaduaLJScaler method) prepare_mdp_from_template() (mstk.wrapper.GMX method) Psf (class in mstk.topology)

Q

qinc_terms (mstk.forcefield.ForceField attribute) queue (mstk.scheduler.PbsJob attribute) (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute)

R

rdmol (mstk.topology.Molecule property) read_frame() (mstk.trajectory.CombinedTrj method) (mstk.trajectory.Dcd method) (mstk.trajectory.Gro method) (mstk.trajectory.LammpsTrj method) (mstk.trajectory.Trajectory method) (mstk.trajectory.TrjHandler method) (mstk.trajectory.Xtc method) (mstk.trajectory.Xyz method) read_frame_from_file() (mstk.trajectory.Trajectory static method) read_frames() (mstk.trajectory.Trajectory method) refresh_residues() (mstk.topology.Molecule method) register() (mstk.forcefield.FFTermFactory static method) (mstk.topology.VirtualSite static method) register_format() (mstk.topology.Topology static method) (mstk.trajectory.TrjHandler static method) registor_format() (mstk.forcefield.ForceField static method) remark (mstk.topology.Topology attribute) remote_dir (mstk.scheduler.RemoteSlurm attribute) RemoteSlurm (class in mstk.scheduler) remove_atom() (mstk.topology.Molecule method) remove_atoms() (mstk.topology.Molecule method) remove_connectivity() (mstk.topology.Molecule method)

remove_drude_particles() (mstk.topology.Molecule method) (mstk.topology.Topology method) remove_non_polar_hydrogens() (mstk.topology.Molecule method) remove_residue() (mstk.topology.Molecule method) remove_virtual_sites() (mstk.topology.Molecule method) (mstk.topology.Topology method) replicate_gro() (mstk.wrapper.GMX method) report() (mstk.ommhelper.reporter.CheckpointReporter method) (mstk.ommhelper.reporter.DrudeTemperatureReporter method) (mstk.ommhelper.reporter.GroReporter method) (mstk.ommhelper.reporter.StateDataReporter method) (mstk.ommhelper.reporter.ViscosityReporter method) repulsion (mstk.forcefield.MieTerm attribute) reset() (mstk.trajectory.Frame method) Residue (class in mstk.topology) residue (mstk.topology.Atom property) residues (mstk.topology.Molecule property) (mstk.topology.Topology property) resize() (mstk.trajectory.Frame method) restore_settings() (mstk.forcefield.ForceField method) restrain_particle_number() (in module mstk.ommhelper.force) run_gjf() (mstk.wrapper.Gauss method) RUNNING (mstk.scheduler.PbsJob.State attribute)

S

save_to() (mstk.forcefield.Zff static method) (mstk.forcefield.Zfp static method) (mstk.topology.GroTopology static method) (mstk.topology.Pdb static method) (mstk.topology.Psf static method) (mstk.topology.Topology static method) (mstk.topology.XyzTopology static method) scale() (mstk.forcefield.PaduaLJScaler method) scale_14_coulomb (mstk.forcefield.ForceField attribute) scale_14_vdw (mstk.forcefield.ForceField attribute) scale_box() (mstk.topology.Topology method) (mstk.wrapper.GMX static method) scale_lj() (mstk.forcefield.PaduaLJScaler method) scale_sigma (mstk.forcefield.PaduaLJScaler attribute) scale_with_packmol() (mstk.topology.Topology method) Scheduler (class in mstk.scheduler) SDKAngleTerm (class in mstk.forcefield) select_com() (mstk.wrapper.GMX method) set_box() (mstk.topology.UnitCell method) set_positions() (mstk.topology.Molecule method) (mstk.topology.Topology method) SETTING_ATTRS (mstk.forcefield.ForceField attribute) sh (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute)

sigma (mstk.forcefield.LJ126Term attribute) (mstk.forcefield.MieTerm attribute) SINGLE (mstk.topology.Bond.Order attribute) size (mstk.topology.UnitCell property) slab_correction() (in module mstk.ommhelper.force) Slurm (class in mstk.scheduler) Smi (class in mstk.topology) split() (mstk.topology.Molecule method) split_residues() (mstk.topology.Molecule method) spring_self() (in module mstk.ommhelper.force) state (mstk.scheduler.PbsJob attribute) state_str (mstk.scheduler.PbsJob attribute) StateDataReporter (class in mstk.ommhelper.reporter) step (mstk.trajectory.Frame attribute) submit() (mstk.scheduler.RemoteSlurm method) (mstk.scheduler.Scheduler method) (mstk.scheduler.Slurm method) submit_cmd (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Slurm attribute) symbol (mstk.topology.Atom attribute) System (class in mstk.simsys)

T

theta (mstk.forcefield.AngleTerm attribute) (mstk.forcefield.HarmonicAngleTerm attribute) (mstk.forcefield.LinearAngleTerm attribute) (mstk.forcefield.SDKAngleTerm attribute) thole (mstk.forcefield.DrudeTerm attribute) (mstk.topology.Atom attribute) time (mstk.trajectory.Frame attribute) TIP4PSite (class in mstk.topology) TIP4PSiteTerm (class in mstk.forcefield) to_omm_system() (mstk.simsys.System method) to_omm_topology() (mstk.topology.Topology method) to_opls_term() (mstk.forcefield.PeriodicDihedralTerm method) to_periodic_term() (mstk.forcefield.OplsDihedralTerm method) to_str() (mstk.chem.formula.Formula method) to_zff() (mstk.forcefield.FFTerm method) (mstk.forcefield.PeriodicDihedralTerm method) to_zff_header() (mstk.forcefield.FFTerm method) to_zfp() (mstk.forcefield.FFTerm method) Topology (class in mstk.topology) topology (mstk.simsys.System property) (mstk.topology.GroTopology attribute) (mstk.topology.LammpsData attribute) (mstk.topology.Molecule property) (mstk.topology.Pdb attribute) (mstk.topology.Psf attribute) (mstk.topology.Smi attribute) (mstk.topology.XyzTopology attribute) (mstk.topology.Zmat attribute) traj_com() (mstk.wrapper.GMX method) Trajectory (class in mstk.trajectory) TRIPLE (mstk.topology.Bond.Order attribute) TrjHandler (class in mstk.trajectory) type (mstk.forcefield.DrudeTerm attribute) (mstk.forcefield.PolarizableTerm attribute) (mstk.forcefield.TIP4PSiteTerm attribute) (mstk.forcefield.VirtualSiteTerm attribute) (mstk.topology.Atom attribute) type() (mstk.forcefield.typer.Typer method) type1 (mstk.forcefield.AngleTerm attribute) (mstk.forcefield.BondTerm attribute) (mstk.forcefield.ChargeIncrementTerm attribute) (mstk.forcefield.DihedralTerm attribute) (mstk.forcefield.HarmonicAngleTerm attribute) (mstk.forcefield.HarmonicBondTerm attribute) (mstk.forcefield.HarmonicImproperTerm attribute) (mstk.forcefield.ImproperTerm attribute) (mstk.forcefield.LinearAngleTerm attribute) (mstk.forcefield.LJ126Term attribute) (mstk.forcefield.MieTerm attribute) (mstk.forcefield.MorseBondTerm attribute) (mstk.forcefield.OplsDihedralTerm attribute) (mstk.forcefield.OplsImproperTerm attribute) (mstk.forcefield.PeriodicDihedralTerm attribute) (mstk.forcefield.SDKAngleTerm attribute) (mstk.forcefield.VdwTerm attribute)

type2 (mstk.forcefield.AngleTerm attribute) (mstk.forcefield.BondTerm attribute) (mstk.forcefield.ChargeIncrementTerm attribute) (mstk.forcefield.DihedralTerm attribute) (mstk.forcefield.HarmonicAngleTerm attribute) (mstk.forcefield.HarmonicBondTerm attribute) (mstk.forcefield.HarmonicImproperTerm attribute) (mstk.forcefield.ImproperTerm attribute) (mstk.forcefield.LinearAngleTerm attribute) (mstk.forcefield.LJ126Term attribute) (mstk.forcefield.MieTerm attribute) (mstk.forcefield.MorseBondTerm attribute) (mstk.forcefield.OplsDihedralTerm attribute) (mstk.forcefield.OplsImproperTerm attribute) (mstk.forcefield.PeriodicDihedralTerm attribute) (mstk.forcefield.SDKAngleTerm attribute) (mstk.forcefield.VdwTerm attribute) type3 (mstk.forcefield.AngleTerm attribute) (mstk.forcefield.DihedralTerm attribute) (mstk.forcefield.HarmonicAngleTerm attribute) (mstk.forcefield.HarmonicImproperTerm attribute) (mstk.forcefield.ImproperTerm attribute) (mstk.forcefield.LinearAngleTerm attribute) (mstk.forcefield.OplsDihedralTerm attribute) (mstk.forcefield.OplsImproperTerm attribute) (mstk.forcefield.PeriodicDihedralTerm attribute) (mstk.forcefield.SDKAngleTerm attribute) type4 (mstk.forcefield.DihedralTerm attribute) (mstk.forcefield.HarmonicImproperTerm attribute) (mstk.forcefield.ImproperTerm attribute) (mstk.forcefield.OplsDihedralTerm attribute) (mstk.forcefield.OplsImproperTerm attribute) (mstk.forcefield.PeriodicDihedralTerm attribute) type_H (mstk.forcefield.TIP4PSiteTerm attribute) type_masses (mstk.topology.LammpsData attribute) type_names (mstk.topology.LammpsData attribute) type_O (mstk.forcefield.TIP4PSiteTerm attribute) Typer (class in mstk.forcefield.typer)

U

UnitCell (class in mstk.topology) UNSPECIFIED (mstk.topology.Bond.Order attribute) update_molecules() (mstk.topology.Topology method) upload() (mstk.scheduler.RemoteSlurm method) (mstk.scheduler.Scheduler method)

use_pbc (mstk.simsys.System attribute) user (mstk.scheduler.PbsJob attribute) username (mstk.scheduler.RemoteSlurm attribute) (mstk.scheduler.Scheduler attribute) (mstk.scheduler.Slurm attribute)

V

value (mstk.forcefield.ChargeIncrementTerm attribute) vdw_classes (mstk.simsys.System attribute) vdw_cutoff (mstk.forcefield.ForceField attribute) vdw_long_range (mstk.forcefield.ForceField attribute) (mstk.forcefield.ForceField property) VDW_LONGRANGE_CORRECT (mstk.forcefield.ForceField attribute) VDW_LONGRANGE_SHIFT (mstk.forcefield.ForceField attribute) vdw_terms (mstk.forcefield.ForceField attribute) VdwTerm (class in mstk.forcefield) vectors (mstk.topology.UnitCell property) velacc() (mstk.wrapper.GMX method)

velocities (mstk.trajectory.Frame attribute) version (mstk.forcefield.FFTerm attribute) (mstk.wrapper.GMX attribute) virtual_site (mstk.topology.Atom attribute) virtual_site_terms (mstk.forcefield.ForceField attribute) VirtualSite (class in mstk.topology) VirtualSiteTerm (class in mstk.forcefield) ViscosityReporter (class in mstk.ommhelper.reporter) volume (mstk.topology.UnitCell property) vsite_pairs (mstk.simsys.System attribute) vsite_types (mstk.simsys.System attribute)

W

wall_lj126() (in module mstk.ommhelper.force) wall_power() (in module mstk.ommhelper.force) workdir (mstk.scheduler.PbsJob attribute) write() (mstk.forcefield.ForceField method) (mstk.topology.Topology method) write_frame() (mstk.trajectory.Dcd method) (mstk.trajectory.Gro method) (mstk.trajectory.Trajectory method) (mstk.trajectory.TrjHandler method) (mstk.trajectory.Xtc method) (mstk.trajectory.Xyz method)

writeFile() (mstk.ommhelper.GroFile static method)

X

xlo (mstk.topology.LammpsData attribute) Xtc (class in mstk.trajectory)

Xyz (class in mstk.trajectory) XyzTopology (class in mstk.topology)

Y

ylo (mstk.topology.LammpsData attribute)

Z

Zff (class in mstk.forcefield) Zfp (class in mstk.forcefield)

ZftTyper (class in mstk.forcefield.typer) zlo (mstk.topology.LammpsData attribute) Zmat (class in mstk.topology)