OutOfPlaneSite¶
- class openmm.openmm.OutOfPlaneSite(*args)¶
This is a VirtualSite that computes the particle location based on three other particles’ locations. If r<sub>1</sub> is the location of particle 1, r<sub>12</sub> is the vector from particle 1 to particle 2, and r<sub>13</sub> is the vector from particle 1 to particle 3, then the virtual site location is given by
r<sub>1</sub> + w<sub>12</sub>r<sub>12</sub> + w<sub>13</sub>r<sub>13</sub> + w<sub>cross</sub>(r<sub>12</sub> x r<sub>13</sub>)
The three weight factors are user-specified. This allows the virtual site location to be out of the plane of the three particles. Note that while w<sub>12</sub> and w<sub>13</sub> are unitless, w<sub>cross</sub> has units of inverse distance.
- __init__(self, particle1, particle2, particle3, weight12, weight13, weightCross) → OutOfPlaneSite¶
- __init__(self, other) → OutOfPlaneSite
Create a new OutOfPlaneSite virtual site.
- Parameters
particle1 (int) – the index of the first particle
particle2 (int) – the index of the second particle
particle3 (int) – the index of the third particle
weight12 (double) – the weight factor for the vector from particle1 to particle2
weight13 (double) – the weight factor for the vector from particle1 to particle3
weightCross (double) – the weight factor for the cross product
Methods
__init__
(-> OutOfPlaneSite)Create a new OutOfPlaneSite virtual site.
getNumParticles
(self)Get the number of particles this virtual site depends on.
getParticle
(self, particle)Get the index of a particle this virtual site depends on.
getWeight12
(self)Get the weight factor for the vector from particle1 to particle2.
getWeight13
(self)Get the weight factor for the vector from particle1 to particle3.
getWeightCross
(self)Get the weight factor for the cross product.
Attributes
The membership flag
- property thisown¶
The membership flag
- getWeight12(self) → double¶
Get the weight factor for the vector from particle1 to particle2.
- getWeight13(self) → double¶
Get the weight factor for the vector from particle1 to particle3.
- getWeightCross(self) → double¶
Get the weight factor for the cross product.
- getNumParticles(self) → int¶
Get the number of particles this virtual site depends on.
- getParticle(self, particle) → int¶
Get the index of a particle this virtual site depends on.
- Parameters
particle (int) – the particle to get (between 0 and getNumParticles())
- Returns
the index of the particle in the System
- Return type
int