22.214.171.124 Static Properties of Atoms
The following table describes the syntax and function of the various
properties available for atoms.
- X coordinate of atom.
- Y coordinate of atom.
- Z coordinate of atom.
- Distance of atom from geometric center. When this property is computed
for a difference table, it returns the length of the vector between the
two atoms being compared. If either atom in the pair has an undefined
position, then the distance will be calculated as zero.
- Sequence number of atom.
- `ENERGY, FORCE'
- The total potential energy (or force) per atom. This is calculated as
follows: we start with the non-bonded energy per atom. The energy of
each bond is split evenly among the two atoms. The bond angle energy is
summed onto the central atom. The torsion angle energy is split between
the center two atoms. The improper torsion energy is summed to the
center atom. The harmonic constraint energy is is added to every atom.
Finally, the hydrogen bond energy is split between the donor and
acceptor atom. FORCE is magnitude of the force vector at each atom
(sqrt((dE/dx)^2 + (dE/dy)^2 + (dE/dz)^2)). The individual force terms
are summed prior to calculating the magnitude.
- `EB, FB'
- Bond energy (or force) per atom - the energy of each bond split evenly
among two atoms is summed for each each atom.
- `ET, FT'
- Angle energy (or force) per atom - The sum of the energies of all angles
whose central atom is the atom.
- `EP, FP'
- Torsion angle energy (or force) per atom - The energy of each torsion
angle is split among the two central atoms and summed over all the
- `EI, FI'
- Improper torsion angle energy (or force) per atom. The energy of all
improper torsions is summed onto the center atom.
- `EHB, FHB'
- Hydrogen bond energy (or force) per atom - The energy of each hydrogen
bond is split across each atom in the pair.
- `EVDW, FVDW'
- Van der Waals energy (or force) per atom - calculated the same way as
- `ELEC, FELE'
- Electrostatic energy (or force) per atom - this is calculated by taking
the pairwise electrostatic energy for each non-bonded pair and summing
half of this energy on each atom in the pair.
- `ELED, FELD'
- Direct part of the electrostatic interaction. This is the same as
ELEC if reaction fields are not being calculated.
- `ERXN, FRXN'
- The reaction field energy (or force). WARNING: the reaction
field calculation was under development in CHARMM v.16. Please review
the code before attempting any calculations with this option.
- `ENB, FNB'
- Non-bonded energy (or force) per atom - sum of EVDW and
- `EC, FC'
- Harmonic constraint energy, or force.
- `EUSER, FUSER'
- The energy (or force) returned by the
See CONGEN Modifications, for a description of
provides more information on writing user energy routines. Note that the
USERE routine must be written to return the appropriate data for
analysis of energies (versions of
USERE routines which do not
support the analysis of energies will run in the main part of the
program even though they will bomb out if called from analysis).
- The electrostatic energy of each atom as calculated by the Poisson-Boltzmann
equation. This calculation is done by creating an empty charge density array,
looping through each atom in the system, charging the array specifically for each
atom, and calculating the electrostatic energy, see PBE ENERGY Command.
- The actual dielectric constant for each atom as used by the Poisson-Boltzmann
equation. This property is useful for checking the effects
of adjusting dielectric constants based on exposed surfaces,
see PBE SETUP Command.
- The accessible surface of the atom in square Angstroms as calculated by
Lee and Richard's accessible surface program. A probe diameter of 1.4 A
is used with a fractional error parameter of 0.05. These two parameters
can be changed using the analysis set command, see Analysis Set Command. This surface includes the radius of the probe.
- The contact area as calculated by Lee and Richard's accessible surface program1.
The contact area does not include the radius of the probe. The
parameters are the same as in the SURFACE property.
- The Van Der Waals radius of the atom as used in the non-bonded energy
- The charge of the atom.
- The polarizability of the atom as used in the non-bonded energy
- The effective number of electrons as used in the non-bonded energy
- `VSGEPOL, ASGEPOL, MSGEPOL'
These three table properties use the GEPOL
algorithm2345 to calculate three different surface
properties of the atoms; van der Waals, accessible, and molecular
surfaces. The van der Waals surface (keyword VSGEPOL) is the
surface of the atoms calculated using the van der Waals radii and
accessibility is ignored. The accessible surface (keyword
ASGEPOL) is the area of the locus of the center of water probe. It
is the same surface as calculated by the Lee and Richards algorithm
referenced above. The molecular surface (keyword MSGEPOL) is the
locus of points on the surface of the probe sphere when the probe is in
contact with at least one atom in the molecule.
When calculating van der Waals and accessible surfaces, the GEPOL
algorithm uses a points on tesselated sphere to calculate what parts of
the sphere are exposed, and it adds all the contributions of the
tesserae to determine the surface. The calculation of the molecular
surface uses this accessible surface algorithm, but additional spheres
are added to the calculation of the accessible surface, and these
additional spheres closely define the molecular surface.
The GEPOL command, see Gepol Command, may be used to set
operating parameters for the GEPOL algorithm.
- `RVSGEPOL, RASGEPOL, RMSGEPOL'
- These three table properties are the “relative” equivalents of
VSGEPOL, ASGEPOL, and MSGEPOL. In this context, “relative”
means relative to the surface area
of a sphere of radius equal to the atomic radius in the
case of the van der Waals surface and molecular surface, and
relative to a sphere of radius equal to the atomic radius plus the solvent
probe radius in the case of the accessible surface.