write

Note

This command has been ported to the new APBS syntax (see YAML- and JSON-format input files); see generic.WriteMap and specific functions for different calculations:

• Finite differences; see finite_difference.write_atom_potentials().

• Finite elements; see finite_elements.write_atom_potentials().

This controls the output of scalar data calculated during the Poisson-Boltzmann run. This keyword can be repeated several times to provide various types of data output from APBS. The syntax is:

write {type} {format} {stem}

type

A string indicating what type of data to output:

charge

Write out the biomolecular charge distribution in units of e_c (electron charge) per ų (multigrid only).

pot

Write out the electrostatic potential over the entire problem domain in units of k_b T e_c^-1 (multigrid and finite element), where

k_b

Boltzmann’s constant: 1.3806504 × 10⁻²³ J K^-1

T

The temperature of your calculation in K

e_c

is the charge of an electron: 1.60217646 × 10^-19 C

As an example, if you ran your calculation at 300 K, then the potential would be written out as multiples of k_b T e_c^-1 = (1.3806504 × 10⁻²³ J K^-1) × (300 K) × (1.60217646 × 10^-19 C)^-1 = (4.1419512 × 10^-21 J) × (6.241509752 × 10¹⁸ C^-1) = 25.85202 mV

atompot

Write out the electrostatic potential at each atom location in units of k_b T e_c^-1 (multigrid and finite element).

smol

Write out the solvent accessibility defined by the molecular surface definition (see srfm (elec) smol). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element).

sspl

Write out the spline-based solvent accessibility (see srfm (elec) spl2). Values are unitless and range from 0 (inaccessible) to 1 (accessible) (multigrid and finite element)

vdw

Write out the van der Waals-based solvent accessibility (see srfm (elec) smol with srad 0.0). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element)

ivdw

Write out the inflated van der Waals-based ion accessibility (see srfm (elec) smol). Values are unitless and range from 0 (inaccessible) to 1 (accessible). (multigrid and finite element)

lap

Write out the Laplacian of the potential \(\nabla^2 \phi\) in units of k_B T e_c^-1 Å^-2 (multigrid only).

edens

Write out the “energy density” \(-\nabla \cdot \epsilon \nabla \phi\) in units of k_B T e_c^-1 Å^-2 (multigrid only).

ndens

Write out the total mobile ion number density for all ion species in units of M (multigrid only). The output is calculated according to the formula (for nonlinear PB calculations): \(\rho(x) = \sum_i^N {\bar{\rho}_i e^{-q_i\phi(x) - V_i (x)}}\), where N is the number of ion species, \(\bar{\rho}_i\) is the bulk density of ion species i, \(q_i\) is the charge of ion species i, \(\phi(x)\) is the electrostatic potential, and \(V_i\) is the solute-ion interaction potential for species i.

qdens

Write out the total mobile ion charge density for all ion species in units of e_c M (multigrid only). The output is calculated according to the formula (for nonlinear PB calculations): \(\rho(x) = \sum_i^N {\bar{\rho}_i q_i e^{-q_i\phi(x) - V_i (x)}}\), where N is the number of ion species, \(\bar{\rho}_i\) is the bulk density of ion species i, \(q_i\) is the charge of ion species i, \(\phi(x)\) is the electrostatic potential, and \(V_i\) is the solute-ion interaction potential for species i.

dielx or diely or dielz

Write out the dielectric map shifted by 1/2 grid spacing in the {x, y, z}-direction (see READ input file section diel). The values are unitless (multigrid only).

format

A string that specifies the format for writing out the data:

dx

Write out data in OpenDX scalar data format. This is the preferred format for APBS I/O. (multigrid and finite element).

avs

Write out data in AVS UCD format. (finite element only).

uhbd

Write out data in UHBD scalar data format. (multigrid only).

gz

Write out OpenDX scalar data format in gzipped (zlib) compatible format. Appends .dx.gz to the filename.

flat

Write out data as a plain text file. (multigrid and finite element).

stem

A string that specifies the path for the output; files are written to stem.XYZ, where XYZ is determined by the file format (and processor rank for parallel calculations). If the pathname contains spaces, then it must be surrounded by double quotes.