pair_style lj/cleavcutsqlmod

Syntax

pair_style lj/cleavcutsqlmod cut-off lambda i_IDflag orientation alpha

  • cutoff = global internal cut-off

  • lambda = global scaling of the potential

  • i_IDflag = new (integer) property to be added to the atoms

  • orientation = direction perpendicular to the cleaving plane

  • alphaLJ = damping parameter (inverse distance units)

pair_coeff accepts only the following arguments

pair_coeff a b lambda

where

a       = atom of type a [mandatory]
b       = atom of type b [mandatory]
epsilon = energy constant (energy units)
sigma   = VdW radius (distance units)
lambda  = scaling of the potential

This pair style is derived from the pair/ljcut in LAMMPS and we refer to the LAMMPS documentation for the description of its main features. Here, only the modifications needed for the cleaving calculations will be considered.

This pair style modifies the Lennard-Jones potential as proposed by 1 in order to avoid the “Lennard-Jones catastrophe”. The potential is modified as:

\[ U(r_{ln}) = 4 \lambda\epsilon\left(\frac{1}{\left(\alpha_{LJ}(1-\lambda)^2+\left(\frac{r_{ln}}{\sigma}\right)^{6}\right)^2} -\frac{1}{\left(\alpha_{LJ}(1-\lambda)^2+\frac{r_{ln}}{\sigma}^{6}\right)^2} \right),\;\mbox{if}\; r_{ln} \leq r_c \]

where \(r_{ln}=|\mathbf{r}_l-\mathbf{r}_n|\) for each couple of atoms \(l,n\) in the system and \(r_c\) is the cut-off for the potential.

The description of the cleaving methodology using this pair style is analogous to the one described for the pair style coul/dsf[cleav] to which we refer.

1

T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, and W. F. Van Gunsteren. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chemical physics letters, 222(6):529–539, 1994.