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fix filter/corotate command

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Syntax

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fix ID group-ID filter/corotate keyword value ...
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  • ID, group-ID are documented in fix command

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    • +

  • one or more constraint/value pairs are appended

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    • +

  • constraint = b or a or t or m

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    +b values = one or more bond types
+a values = one or more angle types
+t values = one or more atom types
+m value = one or more mass values
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    • +
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Examples

+
timestep 8
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+fix cor all filter/corotate m 1.0
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+fix cor all filter/corotate b 4 19 a 3 5 2
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Description

+

This fix implements a corotational filter for a mollified impulse +method. In biomolecular simulations, it allows the usage of larger +timesteps for long-range electrostatic interactions. For details, see +(Fath).

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When using run_style respa for a biomolecular +simulation with high-frequency covalent bonds, the outer time-step is +restricted to below ~ 4fs due to resonance problems. This fix filters +the outer stage of the respa and thus a larger (outer) time-step can +be used. Since in large biomolecular simulations the computation of +the long-range electrostatic contributions poses a major bottleneck, +this can significantly accelerate the simulation.

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The filter computes a cluster decomposition of the molecular structure +following the criteria indicated by the options a, b, t and m. This +process is similar to the approach in fix shake, +however, the clusters are not kept contrained. Instead, the position +is slightly modified only for the computation of long-range forces. A +good cluster decomposition constitutes in building clusters which +contain the fastest covalent bonds inside clusters.

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If the clusters are chosen suitably, the run_style respa is stable for outer time-steps of at least 8fs.

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

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No information about these fixes is written to binary restart files. None of the fix_modify options +are relevant to these fixes. No global or per-atom quantities are +stored by these fixes for access by various output commands. No parameter of these fixes +can be used with the start/stop keywords of the run +command. These fixes are not invoked during energy minimization.

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Restrictions

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This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.

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Currently, it does not support molecule templates.

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