fix filter/corotate command
fix ID group-ID filter/corotate keyword value ...
ID, group-ID are documented in fix command
one or more constraint/value pairs are appended
constraint = b or a or t or m
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
timestep 8 run_style respa 3 2 8 bond 1 pair 2 kspace 3 fix cor all filter/corotate m 1.0 fix cor all filter/corotate b 4 19 a 3 5 2
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).
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.
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.
If the clusters are chosen suitably, the run_style respa is stable for outer time-steps of at least 8fs.
Restart, fix_modify, output, run start/stop, minimize info:
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.