fepdualtop

singletopology

Enables single-topology FEP; dual-topology is the default.

block1

Defines the group of atoms that vanish (decouple) during the FEP simulation.

Value	Atom range
Default	None

block2

Defines the group of atoms that appear (couple) during the FEP simulation.

Value	Atom range
Default	None

fep_scheme

Value	pi: parameter interpolation.
	ei: energy interpolation.
Default	pi

Defines the strategy for scaling reciprocal-space electrostatic interactions when PME is used. The conventional approach employs energy interpolation: two PME evaluations are performed per time step, and the long-range electrostatic energy of the perturbed system is obtained by combining the two results as follows:

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

“LR” stands for long-range electrostatic interactions, while “A”, “B”, and “C” refer to atoms in the vanishing part, appearing part, and environment, respectively.

Alternatively, a more efficient parameter-interpolation scheme can be used to treat long-range electrostatic interactions. In this approach, the force-field parameters—specifically, the charges of the vanishing and appearing atoms—are scaled and evaluated 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

Defines the number of molecular dynamics steps used for system equilibration per lambda window.
Data generated during equilibration will not be recorded.

Value	An integer
Default	0

num_lambda_windows

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

Value	An integer
Default	2

start_window

Defines the index of the lambda window from which the simulation begins.
A positive integer is required.

Value	An integer
Default	1

end_window

Defines the index of the lambda window at which the simulation ends.

Value	An integer
Default	Should be the same as num_lambda_windows

fepout_freq

The frequency (in MD steps) at which energy components are printed for ensemble averaging.

Value	An integer
Default	1

col_coupledstartwindow

Value	An integer
Default	0

Defines the index of the lambda window after which the electrostatic interactions of appearing atoms begin to be considered. For vanishing atoms, their electrostatic interactions are gradually scaled to zero from the first window to col_coupledstartwindow (see the illustration below).
The default value 0 disables this keyword, meaning that coupling and decoupling of electrostatic interactions occur across all FEP windows.

This option is designed to ease the so-called end-point catastrophe problem, which arises from the rapid decay of van der Waals (vdW) interactions compared to electrostatic interactions.
One can imagine that if the vdW interactions between two oppositely charged atoms are scaled close to zero, their remaining significant electrostatic attraction may cause them to overlap, leading to numerical instability.
The logic behind this option is to decouple the electrostatic interactions before the vdW interactions become too weak.

annihilation

Flag used to indicate whether the intra-fragment bonds involving vanishing or appearing atoms are perturbed.
By default, the program assumes no perturbation of intra-fragment bonds.

nointradecouple

Do not decouple the non-bonded interactions between atoms within the vanishing or appearing fragment.
By default, the program does decouple non-bonded interactions within the two end states (i.e., nointradecouple is false).

lj_lambda_go

Lambda array used to decouple the van der Waals interactions of vanishing atoms with the environment.
If the value of lj_lambda_go is x, the interactions involving block 1 atoms are scaled by (1.0 - x).

lj_lambda_in

Lambda array used to couple the van der Waals interactions of appearing atoms with the environment.
If the value of lj_lambda_in is x, the interactions involving block 2 atoms are scaled by x.

col_lambda_go

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

col_lambda_in

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

alpha_soft

Value	A real number
Default	0.

Defines the parameter (radius shifting coefficient) used in the modified soft-core van der Waals potential.
The distance between two interacting atoms is shifted from r^2 to r^2 + \alpha * (1 - \lambda) when the interaction is scaled by \lambda.

beta_soft

Value	A real number
Default	0.

Defines the parameter (radius shifting coefficient) used in the modified soft-core Coulombic potential.
Similar to alpha_soft for van der Waals interactions.