Truncation Panel
The Truncation panel defines the non-bonded cutoffs settings for a QSite calculation.
To open this panel, click the Settings button for Use non-bonded cutoffs in the Potential tab of the QSite panel.
The use of non-bonded cutoffs to remove interactions between widely separated pairs of atoms is an important strategy for reducing the time and memory required to perform calculations on large systems. At present only residue-based cutoffs are supported for calculations set up in Maestro. This means that all atoms within complete residues that have any pair of atoms within the cutoff distance will be included in the non-bonded interaction list. The list is updated periodically as the geometry changes, because residues may move inside or beyond the cutoff radius.
- Features
- Additional Resources
Truncation Panel Features
- Update neighbor-list frequency (#steps)
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This text box specifies the number of steps after which the neighbor list is updated. All pairs of atoms that fall within the cutoff radius are stored in a "neighbor list". When the geometry of the structure changes, some pairs of atoms that were originally outside the cutoff distance may move within the cutoff, and others may move outside the cutoff distance. Consequently, the neighbor list needs to be updated from time to time. The frequency of this update is controlled by this integer field. By default the neighbor list is updated every 10 minimization steps. Increasing this value (updating the neighbor list less often) will speed up the calculation but may affect the accuracy of the results. Decreasing this value (updating the neighbor list more often) will slow down the calculation but may improve the accuracy.
- Residue-based cutoff distance
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This text box specifies the value for the cutoff distance.All atoms in complete residues that have any pair of atoms within this distance are included in the nonbonded interaction list. Increasing the cutoff distance will slow the calculation and require more memory, but may yield more accurate results. Decreasing the cutoff will speed up the calculation, but may reduce the accuracy of the results if significant non-bonded interactions are omitted. This is especially true for systems that include formally charged atoms, as such systems can have large long-range electrostatic interactions.