Cell Size Requirements for Isolated Systems

Calculations of isolated systems (i.e. decoupling of the electrostatic images in the Poisson solver) are activated by using the keyword SYMMETRY with the option ISOLATED SYSTEM or 0.

The box is assumed to be orthorhombic, i.e. all angles have to be 90$^{\circ}$ . With the additional options SURFACE or POLYMER periodic boundary conditions in only one or two dimensions, respectively, are decoupled. Available Poisson solvers are: {HOCKNEY,TUCKERMAN,MORTENSEN}

All methods require that the charge density is zero at the border of the box. For normal systems this means that about a minimum of 3 Angstrom space between the outmost atoms and the box is required. However, for some systems (e.g. with negative CHARGE) and for high accuracy calculations this may not be enough. Some a list of additional requirements of the individual methods follows below.

The ISOLATED MOLECULE keyword has only an effect on the calculation of the degrees of freedom (3N-6 vs. 3N-3 for periodic systems) and thus the calculation of the instantaneous temperature.

CENTER MOLECULE ON/OFF: The main purpose of this is to center the molecule (center of mass) in the box. This is needed for the HOCKNEY Poisson solver. This solver gives wrong results if the charge density is not centered in the computational box. All other solvers behave like the periodic counterpart, i.e. the relative position of the charge density and the box are not important. Further requirements:

HOCKNEY Method:

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molecule has to be in the center of the box

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box size molecule + 3 Å border

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expensive for very small systems

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not available for some response calculations

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POLYMER is available but gives (currently, Version 3.9) wrong results.

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SURFACE is available and works.

TUCKERMAN Method:

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box size : molecule + 3 Å border AND 2*size of charge distribution

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expensive for large systems, in some cases smaller boxes might be used without losing too much accuracy

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SURFACE or POLYMER are not available

MORTENSEN Method:

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same as TUCKERMAN, but using analytic formula made possible by using special boundary conditions (sphere, rod)

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SURFACE and POLYMER are available and should be safe to use (MORTENSEN is default for SURFACE and POLYMER)

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If you do an isolated system calculation, your cell has to be cubic, if you use POLYMER cell dimensions b and c have to be equal.

Finally, for many systems using a large enough cell and periodic boundary conditions is also an option. In general, the computed properties of molecules should be independent of the scheme used (either pbc or isolated box) except in difficult cases such as charged molecules, where the calculation in an isolated box is recommended. The PBC calculation is always cheaper for a box of the same size, so for a neutral molecule such as water molecule you would save time and memory by not using SYMMETRY 0.