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Commit d6ebdc03 authored by pinyili2's avatar pinyili2
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add 4-rigidbodies

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...@@ -232,8 +232,9 @@ ...@@ -232,8 +232,9 @@
"## Attaching point particles\n", "## Attaching point particles\n",
"\n", "\n",
"Besides attaching grids to rigid body objects, we can attach point particles that can be subject to all the usual point-particle potentials. We can use this feature, for example, to confine the center of a rigid body, or to connect multiple rigid bodies together, or to add disordered tails to a structured protein. Note that rigid-body attached particles are not written to the particle dcd and their mass/friction is ignored.\n", "Besides attaching grids to rigid body objects, we can attach point particles that can be subject to all the usual point-particle potentials. We can use this feature, for example, to confine the center of a rigid body, or to connect multiple rigid bodies together, or to add disordered tails to a structured protein. Note that rigid-body attached particles are not written to the particle dcd and their mass/friction is ignored.\n",
"The positions of attached particles are defined relative to the rigid body’s own frame, not the lab frame. To attach a particle, first create the particle and then use `rigid_body_type.attach_particle(particle)`. Alternatively, you can provide a list of particles using the `attached_particles` keyword when creating the `RigidBodyType` object.\n",
"\n", "\n",
"The syntax for attaching a particle is simple: First create a particle and then run `rigid_body_type.attach_particle( particle )`, or you can provide a list of particles with the keyword `attached_particles` when you create the RigidBodyType object. One caveat: the attached particles cannot belong to any group, and you should wait to define any bonded interactions or restraints, since these act on particle index, which will be unique for the (copied) particle later attached to each rigid body. Non-bonded interactions and those that involve grids or rigid body potentials can be set up beforehand. Once you've constructed rigid body objects, each one will have the attribute `rigid_body.attached_particles` which you can use to access the particles for use in bonded interactions.\n", "One caveat: the attached particles cannot belong to any group, and you should wait to define any bonded interactions or restraints, since these act on particle index, which will be unique for the (copied) particle later attached to each rigid body. Non-bonded interactions and those that involve grids or rigid body potentials can be set up beforehand. Once you've constructed rigid body objects, each one will have the attribute `rigid_body.attached_particles` which you can use to access the particles for use in bonded interactions.\n",
"\n", "\n",
"As an exercise, see if you can apply a constant force to the SSBs using attached particles subject to a grid-based force." "As an exercise, see if you can apply a constant force to the SSBs using attached particles subject to a grid-based force."
] ]
...@@ -265,7 +266,11 @@ ...@@ -265,7 +266,11 @@
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3", "pygments_lexer": "ipython3",
<<<<<<< HEAD
"version": "3.8.19" "version": "3.8.19"
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"version": "3.11.10"
>>>>>>> 3d65d38cc307f2c7e4a644d446a457480e038be5
} }
}, },
"nbformat": 4, "nbformat": 4,
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