write — APBS-PDB2PQR 1.6 documentation

# write

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:</p>

  `charge`
    Write out the biomolecular charge distribution in units of ec (electron charge) per Å3 (multigrid only).
  `pot`

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

    kb
      Boltzmann’s constant: 1.3806504 × 10−23 J K-1
    T
      The temperature of your calculation in K
    ec
      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 kb T ec-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 kb T ec-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 kB T ec-1 Å-2 (multigrid only).
  `edens`
    Write out the “energy density” \(-\nabla \cdot \epsilon \nabla \phi\) in units of kB T ec-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 ec 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.