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fix spring/chunk command

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Syntax

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fix ID group-ID spring/chunk K chunkID comID
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  • ID, group-ID are documented in fix command
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  • spring/chunk = style name of this fix command
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  • K = spring constant for each chunk (force/distance units)
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  • chunkID = ID of compute chunk/atom command
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  • comID = ID of compute com/chunk command
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Examples

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fix restrain all spring/chunk 100 chunkID comID
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Description

+

Apply a spring force to the center-of-mass (COM) of chunks of atoms as +defined by the compute chunk/atom command. +Chunks can be molecules or spatial bins or other groupings of atoms. +This is a way of tethering each chunk to its initial COM coordinates.

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The chunkID is the ID of a compute chunk/atom command defined in the +input script. It is used to define the chunks. The comID is the ID +of a compute com/chunk command defined in the input script. It is +used to compute the COMs of each chunk.

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At the beginning of the first run or +minimize command after this fix is defined, the +initial COM of each chunk is calculated and stored as R0c, where C is +the chunk number. Thereafter, at every timestep (or minimization +iteration), the current COM of each chunk is calculated as Rc. A +restoring force of magnitude K (Rc - R0c) Mi / Mc is applied to each +atom in each chunk where K is the specified spring constant, Mi is +the mass of the atom, and Mc is the total mass of all atoms in the +chunk. Note that K thus represents the spring constant for the +total force on each chunk of atoms, not for a spring applied to each +atom.

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Restart, fix_modify, output, run start/stop, minimize info

+

No information about this fix is written to binary restart files.

+

The fix_modify energy option is supported by this +fix to add the energy stored in all the springs to the system’s potential +energy as part of thermodynamic output.

+

This fix computes a global scalar which can be accessed by various +output commands. The scalar is the +energy of all the springs, i.e. 0.5 * K * r^2 per-spring.

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The scalar value calculated by this fix is “extensive”.

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No parameter of this fix can be used with the start/stop keywords of +the run command.

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The forces due to this fix are imposed during an energy minimization, +invoked by the minimize command.

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Note

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If you want the spring energies to be included in the total +potential energy of the system (the quantity being minimized), you +MUST enable the fix_modify energy option for this +fix.

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Restrictions

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none
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