TWF¶

class hoomd.md.pair.TWF(nlist, default_r_cut=None, default_r_on=0.0, mode='none')¶

Bases: Pair

Pair potential model for globular proteins.

Parameters:

nlist (hoomd.md.nlist.NeighborList) – Neighbor list.
default_r_cut (float) – Default cutoff radius \([\mathrm{length}]\).
default_r_on (float) – Default turn-on radius \([\mathrm{length}]\).
mode (str) – Energy shifting/smoothing mode.

TWF computes the Ten-wolde Frenkel potential on all particles in the simulation state:

\[U(r) = \frac{4 \epsilon}{\alpha^2} {\left[ {\left(\frac{\sigma^2}{r^2} - 1 \right)}^{-6} - \alpha {\left(\frac{\sigma^2}{r^2} - 1 \right)}^{-3}\right]}\]

The potential was introdcued in Pieter Rein ten Wolde and Daan Frenkel 1997.

Example:

nl = nlist.Cell()
twf = hoomd.md.pair.TWF(nl, default_r_cut=3.0)
twf.params[("A", "A")] = {
    "sigma": 1.0,
    "epsilon": 1.0,
    "alpha": 50.0,
}
twf.r_cut[("A", "B")] = 3.0

Members inherited from AutotunedObject:

property kernel_parameters¶: Kernel parameters. Read more...

property is_tuning_complete¶: Check if kernel parameter tuning is complete. Read more...

tune_kernel_parameters()¶: Start tuning kernel parameters. Read more...

Members inherited from Force:

additional_energy¶: Additional energy term. Read more...

additional_virial¶: Additional virial tensor term \(W_\mathrm{additional}\). Read more...

cpu_local_force_arrays¶: Local force arrays on the CPU. Read more...

energies¶: Energy contribution \(U_i\) from each particle. Read more...

energy¶: The potential energy \(U\) of the system from this force. Read more...

forces¶: The force \(\vec{F}_i\) applied to each particle. Read more...

gpu_local_force_arrays¶: Local force arrays on the GPU. Read more...

torques¶: The torque \(\vec{\tau}_i\) applied to each particle. Read more...

virials¶: Virial tensor contribution \(W_i\) from each particle. Read more...

Members inherited from Pair:

nlist¶: Neighbor list used to compute the pair force. Read more...

mode¶: Energy smoothing/cutoff mode. Read more...

r_cut¶: Cuttoff radius beyond which the energy and force are 0. Read more...

r_on¶: Radius at which the XPLOR smoothing function starts. Read more...

compute_energy()¶: Compute the energy between two sets of particles. Read more...

Members defined in TWF:

params¶

The LJ potential parameters. The dictionary has the following keys:

epsilon (float, required) - energy parameter \(\varepsilon\) \([\mathrm{energy}]\)
sigma (float, required) - particle size \(\sigma\) \([\mathrm{length}]\)
alpha (float, required) - controls well-width \(\alpha\) \([\mathrm{dimensionless}]\)

Type: TypeParameter [tuple [particle_type, particle_type], dict]