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}
typeA 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).
potWrite 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)
smolwith 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.
dielxordielyordielz- 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).
formatA 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, whereXYZis determined by the file format (and processor rank for parallel calculations). If the pathname contains spaces, then it must be surrounded by double quotes.