enedecomp

enedecomp

Perform per-atom energy decomposition.

enedecomp [<name>] 
          [<mask>]
          [out <filename>]
          [savecomponents]
          [pme [cut <cutoff>] [dsumtol <dtol>] [ewcoeff <coeff>] [erfcdx <dx>] [skinnb <skinnb>] [ljswidth <width>] [order <order>] [nfft <nfft1>, <nfft2>,<nfft3>]]

[<name>] Data set name.
[<mask>] Mask of atoms to calculate energy for.
[out <filename> ] File to write results to.
[savecomponents] If specified, also save the individual components of the total energy (bond, angle, dihedral, etc.).
[pme] Use particle mesh Ewald for electrostatics; van der Waals energy will be calculated using a long-range correction for periodicity.
cut <cutoff> Direct space cutoff in Angstroms (default 8.0).
dsumtol <dtol> Direct sum tolerance (default 0.00001). Used to determine Ewald coefficient.
ewcoeff <coeff> Ewald coefficient in 1/Ang.
erfcdx Spacing to use for the ERFC splines (default 0.0002 Ang.).
skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff is cut + skinnb); included in order to maintain consistency with results from sander.
ljswidth <width> If specified, use a force-switching form for the Lennard-Jones calculation from <cutoff>-<width>  to <cutoff>.
order <order> Spline order for charges.
nfft <nfft1>,<nfft2>,<nfft3> Explicitly set the number of FFT grid points in each dimension. Will be determined automatically from unit cell dimensions if not specified.

DataSets created:
<name> Set containing atom index and the corresponding average total energy over frames.
If ‘savecomponents’ is specified:
<name>[bond] Set containing atom index and average bond energy over frames.
<name>[angle] Set containing atom index and average angle energy over frames.
<name>[dih] Set containing atom index and average dihedral energy over frames.
<name>[vdw14] Set containing atom index and average 1-4 van der Waals energy over frames.
<name>[elec14] Set containing atom index and average 1-4 electrostatic energy over frames.
<name>[elec] Set containing atom index and average electrostatic energy over frames.
<name>[vdw] Set containing atom index and average van der Waals energy over frames.

Perform per-atom energy decomposition for selected atoms. The energy is calculated for the entire system but only the energies for selected atoms will be
reported. The energy is composed of the regular bond, angle, torsion, 1-4 nonbonded, and nonbonded terms. If ‘savecomponents‘ is specied, each of the energy components will be saved in addition to the total energy for each atom.

If ‘pme‘ is specied the non-bonded terms will us PME for electrostatics and a long-range periodic correction for van der Waals, otherwise a simple model with no cuto will be used.