fepdualtop

singletopology

Turns on single-topology free energy perturbation. The default is to use the dual-topology alchemical transformation.

block1

Value	Atom range
Default	None

Define the group of atoms decoupled (vanishing) in the FEP simulation.

block2

Value	Atom range
Default	None

Define the group of atoms coupled (appearing) in the FEP simulation.

fep_scheme

Value	pi for parameter interpolation
	ei for energy interpolation
Default	pi

Define the strategy used to scale the reciprocal-space electrostatic interactions when using PME. The convention method is to use energy interpolation strategy, for which two times PME calculations are performed per time step, and then the long-range electrostatic energy of the perturbed system is obtained as a combination:

$U(Col-LR)=(1-{\lambda }_{col})U(A-LR)+{\lambda }_{col}U(B-LR)$

"LR" is short for long-range electrostatic interaction; "A, B, C" denotes those atoms belonging to vanishing part, appearing part and the environment.

Alternatively, one can use the more efficient parameter interpolation scheme to perturb the long range electrostatic interactions. In this scheme, the force field parameters, here the charge of vanishing and appearing atoms, are scaled and treated in a single PME calculation:

$U(Col-LR)=U(LR:q_C,\sqrt{{\lambda }_{col}^A}{q}_A,\sqrt{{\lambda }_{col}^B}{q}_B)$

neglect_steps

Value	An integer
Default	0

Define the number of molecular dynamics steps used for system equilibration per lambda window, and the data during equilibration will not be recorded.

num_lambda_windows

Value	An integer
Default	2

Define the number of lambda windows used to transform one end state to the other end state. A positive integer is needed.

start_window

Value	An integer
Default	1

Define the index of window, from which the simulation begins. A positive integer is needed.

end_window

Value	An integer
Default	The same value with num_lambda_windows

Define the index of window, on which the simulation ends.

fepout_freq

Value	An integer
Default	1

Frequency in MD steps to print the energy component used for ensemble averaging.

col_coupledstartwindow

Value	An integer
Default	0

Define the index of the lambda window, after which the electrostatic interactions of appearing atoms starts to consider. For those vanishing atoms, their electrostatic interactions are steadily scaled to zero from the first window to the col_coupledstartwindow window (see the below illustration Figure). The default value 0 defines that this keyword is useless, and the coupling and decoupling of electrostatic interactions are on throughout all FEP windows.

This option is set to ease the so called end-point catastrophes problem, caused by the rapid decay of van der Waals interactions compared to the electrostatic interactions. One can imagine, if the vdW interactions of two atoms (opposite sign of charge) is scaled to close zero, their remaining non-negligible electrostatic interaction have the chance to pull them overlap and cause numerical instability. The logic of this option is thus to decouple the electrostatic interaction before the vdW interactions become very small.

annihilation

Flag used to define that the intra-fragment bonds formed by those vanishing or appearing atoms are perturbed. Default, the program works in the absence of perturbing the intra-fragment bonds.

nointradecouple

Do not decouple the non-bonded interactions between atoms belonging to the vanishing or appearing fragment. Default, the program works by decouple the non-bonded interactions formed inside the two end states (that is nointradecouple is false).

lj_lambda_go

Lambda array to decouple the Van der Waals interactions of vanishing atoms with the environment. The value of lj_lambda_go being x, means the interactions involving block 1 atoms are scaled by (1.0 - x).

lj_lambda_in

Lambda array to couple the Van der Waals interactions of appearing atoms with the environment. The value of lj_lambda_in being x, means the interactions involving block 2 atoms are scaled by x.

col_lambda_go

Lambda array to decouple the electrostatic interactions of vanishing atoms with the environment.

col_lambda_in

Lambda array to couple the electrostatic interactions of appearing atoms with the environment.

alpha_soft

Value	A real number
Default	0.

Define the parameter (radius shifting coefficient) used in the modified soft-core vdW potential form. The distance of two interactions atoms is reshifted from $r^2$ to $r^2+alpha\ast (1-\lambda )$, when the interaction is scaled by $\lambda$.

beta_soft

Value	A real number
Default	0.

Define the parameter (radius shifting coefficient) used in the modified soft-core Columbic potential form. Similar with alpha_soft.