Index

A

alpha_soft command line option amber_parm7 command line option amber_rst7 command line option

angular_type command line option annihilation command line option

B

beta_soft command line option block1 command line option

block2 command line option

C

charge command line option chrg command line option col_coupledstartwindow command line option col_lambda_go command line option col_lambda_in command line option command line option alpha_soft amber_parm7 amber_rst7 angular_type annihilation beta_soft block1 block2 charge chrg col_coupledstartwindow col_lambda_go col_lambda_in crd density_cov dets_type do_tso dr_cov, [1] dt electrostatic elements end_window energy_cov, [1] epsilon exclude fep_scheme fepout_freq file, [1], [2] fix_angle fix_atoms fix_bond fix_torsion frag, [1] frag1 frag2 gbsa gfn ghost grad_cov, [1] Lbox linear_dependence lj_lambda_go lj_lambda_in loc_cov loc_max_it max_dr max_it max_num_atoms_print mb_level mdin mdout neglect_steps nobsse nodiis nointradecouple num_lambda_windows num_states num_steps, [1], [2] offdiag_correlation orb orb1 orb2 output_freq parameters plumed_fn PMEk print_CHARMM print_GTO_block print_GTO_shell print_MO print_MO_details print_pp qm_region rcutoff rst rswitch scaling14 schwarz, [1] singletopology solvent spin2p1 spin_filp start_window temp temp_nhc_length temp_nhc_tau three_body topology triplet tso_for_guess type, [1], [2], [3], [4] tz uhf use_PBC vel_fn zero_charge_atoms zero_charge_resid zero_threshold

crd command line option

D

density_cov command line option dets_type command line option do_tso command line option

dr_cov command line option, [1] dt command line option

E

electrostatic command line option elements command line option end_window command line option

energy_cov command line option, [1] epsilon command line option exclude command line option

F

fep_scheme command line option fepout_freq command line option file command line option, [1], [2] fix_angle command line option fix_atoms command line option

fix_bond command line option fix_torsion command line option frag command line option, [1] frag1 command line option frag2 command line option

G

gbsa command line option gfn command line option

ghost command line option grad_cov command line option, [1]

L

Lbox command line option linear_dependence command line option lj_lambda_go command line option

lj_lambda_in command line option loc_cov command line option loc_max_it command line option

M

max_dr command line option max_it command line option max_num_atoms_print command line option

mb_level command line option mdin command line option mdout command line option

N

neglect_steps command line option nobsse command line option nodiis command line option nointradecouple command line option

num_lambda_windows command line option num_states command line option num_steps command line option, [1], [2]

O

offdiag_correlation command line option orb command line option orb1 command line option

orb2 command line option output_freq command line option

P

parameters command line option plumed_fn command line option PMEk command line option print_CHARMM command line option print_GTO_block command line option

print_GTO_shell command line option print_MO command line option print_MO_details command line option print_pp command line option

Q

qm_region command line option

R

rcutoff command line option rst command line option

rswitch command line option

S

scaling14 command line option schwarz command line option, [1] singletopology command line option solvent command line option

spin2p1 command line option spin_filp command line option start_window command line option

T

temp command line option temp_nhc_length command line option temp_nhc_tau command line option three_body command line option topology command line option

triplet command line option tso_for_guess command line option type command line option, [1], [2], [3], [4] tz command line option

U

uhf command line option

use_PBC command line option

V

vel_fn command line option

Z

zero_charge_atoms command line option zero_charge_resid command line option

zero_threshold command line option