MindSPONGE
Warning
These are experimental prototypes that are subject to change and/or deletion.
Operations
API Name |
Description |
Supported Platforms |
Add the potential energy caused by angle terms to the total potential energy of each atom. |
|
|
Calculate the energy caused by 3-atoms angle term. |
|
|
Calculate the force exerted by angles made of 3 atoms on the corresponding atoms. |
|
|
Calculate angle force and potential energy together. |
|
|
Add the potential energy caused by simple harmonic bonds to the total potential energy of each atom. |
|
|
Calculate the harmonic potential energy between each bonded atom pair. |
|
|
Calculate the force exerted by the simple harmonic bond on the corresponding atoms. |
|
|
Calculate bond force and harmonic potential energy together. |
|
|
Calculate bond force, harmonic potential energy and atom virial together. |
|
|
Calculate bond force and the virial coefficient caused by simple harmonic bond for each atom together. |
|
|
Calculate the inside-box periodic image of each atom. |
|
|
Calculate the constraint force and virial depends on pressure calculation. |
|
|
Calculate the constraint force in a step with iteration numbers. |
|
|
Calculate the constraint force in each iteration. |
|
|
Calculate the constraint force and virial in each iteration. |
|
|
Calculate the constraint force and virial in a step with iteration numbers. |
|
|
Convert FP32 coordinate to Uint32 coordinate. |
|
|
Add the potential energy caused by Coulumb energy correction for each necessary dihedral 1,4 terms to the total potential energy of each atom. |
|
|
Calculate the Coulumb part of 1,4 dihedral energy correction for each necessary dihedral terms on the corresponding atoms. |
|
|
Calculate the Lennard-Jones and Coulumb energy correction and force correction for each necessary dihedral 1,4 terms together and add them to the total force and potential energy for each atom. |
|
|
Add the potential energy caused by Lennard-Jones energy correction for each necessary dihedral 1,4 terms to the total potential energy of each atom. |
|
|
Calculate the Lennard-Jones and Coulumb energy correction and force correction for each necessary dihedral 1,4 terms together and add them to the total force and potential energy for each atom. |
|
|
Calculate the Lennard-Jones part of 1,4 dihedral energy correction for each necessary dihedral terms on the corresponding atoms. |
|
|
Calculate the Lennard-Jones part of 1,4 dihedral force correction for each necessary dihedral terms on the corresponding atoms. |
|
|
Calculate the Lennard-Jones part and the Coulomb part of force correction for each necessary dihedral 1,4 terms. |
|
|
Add the potential energy caused by dihedral terms to the total potential energy of each atom. |
|
|
Calculate the potential energy caused by dihedral terms for each 4-atom pair. |
|
|
Calculate the force exerted by the dihedral term which made of 4-atoms on the corresponding atoms. |
|
|
Calculate dihedral force and potential energy together. |
|
|
Forward FFT with Three-Dimensional Input. |
|
|
Get coordinate of centroid of each residue. |
|
|
Inverse FFT with Three-Dimensional Input. |
|
|
Calculate the displacement vector of each constrained atom pair. |
|
|
Calculate the Van der Waals interaction energy described by Lennard-Jones potential for each atom. |
|
|
Calculate the Van der Waals interaction force described by Lennard-Jones potential energy for each atom. |
|
|
Calculate the Lennard-Jones force and PME direct force together. |
|
|
Calculate the Lennard-Jones force and PME direct force together for pressure. |
|
|
Calculate the Lennard-Jones force, virial and atom energy together. |
|
|
Calculate the Lennard-Jones force and PME direct force together for pressure. |
|
|
Map all atoms in the same residue to the same periodic box, scale if necessary (usually in pressurestat). |
|
|
Update the coordinate of each atom in the direction of potential for energy minimization. |
|
|
One step of classical leap frog algorithm to solve the finite difference Hamiltonian equations of motion for certain system. |
|
|
One step of classical leap frog algorithm to solve the finite difference Hamiltonian equations of motion for certain system, using Langevin dynamics with Liu's thermostat scheme. |
|
|
One step of classical leap frog algorithm to solve the finite difference Hamiltonian equations of motion for certain system, using Langevin dynamics with Liu's thermostat scheme, but with an maximum velocity limit. |
|
|
Leap frog algorithm to solve the Hamiltonian equations of motion with a maximum velocity limit. |
|
|
Compute the random state of the iteration. |
|
|
Compute the MD temperature. |
|
|
Update (or construct if first time) the Verlet neighbor list for the calculation of short-ranged force. |
|
|
Update (or construct if first time) the Verlet neighbor list for the calculation of short-ranged force. |
|
|
Calculate the Coulumb energy of the system using PME method. |
|
|
Calculate the Coulumb energy of the system using PME method for pressure. |
|
|
Calculate the excluded part of long-range Coulumb force using PME(Particle Meshed Ewald) method. |
|
|
Calculate the excluded part of long-range Coulumb force using PME(Particle Meshed Ewald) method for pressure. |
|
|
Calculate the reciprocal part of long-range Coulumb force using PME(Particle Meshed Ewald) method. |
|
|
Calculate the reciprocal part of long-range Coulumb force using PME(Particle Meshed Ewald) method for pressure. |
|
|
Refresh the box-crossing times of each atom. |
|
|
Refresh the coordinate and velocity of each constrained atom after all iterations have ended. |
|
|
Refresh the unsigned coordinate of each constrained atom in each constrain iteration. |
|
|
Get the average dispersion constant of short range Lennard-Jones interaction, for the subsequent long range correction energy and virial. |
|