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 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
ordiely
ordielz
- 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
, whereXYZ
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.