8.3.2 PBE POTENTIAL Command

Syntax

     PBE POTENTIAL repeat(pbe-potential-options)
     
                               [NODIelectric]
                               [TOLerance real]
                               [RTOLerance real]
     pbe-potential-options ::= [MAXITS int]
                               [HISTsize int]
                               [RADIUS real]
                               [problem-option]
     
     problem-option ::= {LINEar   }
                        {NONLinear}

Function

The PBE POTENTIAL command invokes the Gauss-Siedel PBE solver, and the above options affects how the solution is performed. If the PARALLEL LOOPS command is used, see Parallel Command, the potential will be calculated in parallel across available CPU's on a Silicon Graphic multiprocessor workstation. Parallel efficiency is high. N.B., for large memory jobs running on SGI workstations, it is critically important to set the STACK resource limit down from the default value. See Rlimit Command, for more information.

After the potential is calculated, the PBE energy per atom is calculated and stored in an array for this purpose.

The options have the following meaning:

Option

Purpose

NODIELECTRIC

If this option is specified, the potential is calculated assuming the dielectric is equal to the solvent value, keyword SOLVENT in PBE SETUP Command. The Poisson-Boltzmann equation is not used, but rather the potential contribution from each atom is summed onto each grid point. The boundary is also modified.

TOLERANCE

If the maximum change in any potential value during a cycle over all the grid points is less than the TOLERANCE option, then the solver terminates. Values smaller than 10^-6 are generally too small to be achieved. The default setting is 0.001.

RTOLERANCE

If the RMS of the changes in potential value during a cycle over all the grid points (maximum residuals) is less than this option, the solver terminates. This option is less restrictive than the TOLERANCE option above, and therefore, terminates sooner. The maximum change is typically an order of magnitude bigger than the RMS change. The default setting is 0.0, in which case, the test is not used.

MAXITS

The specifies the maximum number of iterations allowed for the solver. Because of the odd-even checkboard cycling, two iterations are necessary to cover all the grid points. The default is 100.

HISTSIZE

When the PBE solver is working toward a small tolerance, it is possible for a potentially infinite loop to be entered. In order to detect this, CONGEN maintains an array of maximum residuals for twice the number of cycles given by HISTSIZE. At the end of each iteration over all the atoms, the minimum value for the maximum residual for the last HISTSIZE cycles is compared against the minimum for the previous HISTSIZE cycles. If it has not improved, then the PBE solver terminates. Effectively, this mechanism checks for any improvement in the solution of HISTSIZE cycles. The default value is 30.

RADIUS

Overrides the default setting, see Introduction to Poisson-Boltzmann Electrostatics, for the spectral radius. If this value is set to zero, then overrelaxation is not used. If the value is negative, then the absolute value is used as the overrelaxation parameter.

LINEAR

NONLINEAR

These two options control whether the linearized form of the Poisson-Boltzmann equation is solved. Generally, only the linearized form should be used. The non-linear form has a modest radius of convergence, and large charges will result in divergence of the solver. When the non-linear form is used, execution time is much slower, and overrelaxation is turned off. The default is LINEAR.