# energy

Calculate simple bond, angle, dihedral, and non-bonded energy terms (no PME).

energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]] [bond] [angle] [dihedral] {[nb14]|[e14]|[v14]} {[nonbond]|[elec] [vdw]} [{nokinetic|kinetic [ketype {vel|vv}] [dt <dt>]}] [ etype { simple | directsum [npoints <N>] | ewald [cut <cutoff>] [dsumtol <dtol>] [ewcoeff <coeff>] [erfcdx <dx>] [skinnb <skinnb>] [ljswidth <width>] [rsumtol <rtol>] [maxexp <max>] [mlimits <X>,<Y>,<Z>] | pme [cut <cutoff>] [dsumtol <dtol>] [ewcoeff <coeff>] [erfcdx <dx>] [skinnb <skinnb>] [ljswidth <width>] [order <order>] [nfft <nfft1>,<nfft2>,<nfft3>] [ljpme [ewcoefflj <ljcoeff>]] } ]

`[<name>`

] Data set name.

`[<mask1>]`

Mask of atoms to calculate energy for.

`[out <filename>]`

File to write results to.

`[nobondstoh]`

Skip calculating the energy of bonds to hydrogen.

`[bond]`

Calculate bond energy.

`[openmm]`

If specified and CPPTRAJ is compiled with OpenMM support, use OpenMM to calculate energy.

Note: this will only calculate total energy; any keywords pertaining to individual energy components are not available. For a list of potential options that can be used with ‘openmm’ see emin

`[angle]`

Calculate angle energy.

`[dihedral]`

Calculate dihedral energy.

`[nb14]`

Calculate nonbonded 1-4 energy.

`[e14]`

Calculate 1-4 electrostatics.

`[v14]`

Calculate 1-4 van der Waals.

`[nonbond]`

Calculate nonbonded energy (electrostatics and van der Waals).

`[elec]`

Calculate electrostatic energy.

`[vdw]`

Calculate van der Waals energy.

`[nokinetic]`

Do not calculate kinetic energy even if velocity/force information present.

`[kinetic]`

Attempt to calculate kinetic energy. Requires force and/or velocity information.

`ketype {vel|vv}`

Specify kinetic energy type. If not specified, if velocity and force information use a velocity verlet-type calculation (vv), i.e. assume velocities are a half-step ahead of the forces. If only velocity information is present, calculate from on-step velocities (vel).

`dt <dt>`

Time step for vv calculation in ps.

`[etype <type>]`

Calculate electrostatics via specified type.

`[simple]`

Use simple Coulomb term for electrostatics, no cutoff.

`[directsum]`

Use direct summation method for electrostatics.

`[npoints <N>]`

Number of cells in each direction to calculate the direct sum.

`[ewald]`

Use Ewald summation for electrostatics. If van der Waals energy will be calculated a long-range correction for periodicity will be applied.

`cut <cutoff>`

Direct space cutoff in Angstroms (default 8.0).

`dsumtol <dtol>`

Direct sum tolerance (default 0.00001). Used to determine Ewald coefficient.

`rsumtol <rtol>`

Reciprocal sum tolerance (default 0.00005). Used to determine number of reciprocal space vectors.

`ewcoeff <coeff>`

Ewald coefficient in 1/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.

`mlimits <X>,<Y>,<Z>`

Explicitly set the number of reciprocal space vectors in each dimension.

`[pme]`

Use particle mesh Ewald for electrostatics. If van der Waals energy will be calculated a long-range correction for periodicity will be applied.

`cut <cutoff>`

Direct space cutoff in Angstroms (default 8.0).

`dsumtol <dtol>`

Direct sum tolerance (default 0.00001). Used to determine Ewald coefficient.

`ewcoe<coe>`

Ewald coefficient in 1/Ang.

`erfcdx <dx>`

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 <nt1>,<nt2>,<nt3>`

Explicitly set the number of FFT grid points in each dimension. Will be determined automatically if not specified.

`ljpme`

If specified use particle mesh Ewald for calculating Lennard-Jones interactions.

`ewcoej`

Ewald coefficient for Lennard-Jones PME (implies `ljpme`

)

**DataSet Aspects:**

`[bond]`

Bond energy.

`[angle]`

Angle energy.

`[dih]`

Dihedral energy.

`[vdw14]`

1-4 van der Waals energy.

`[elec14]`

1-4 electrostatic energy.

`[vdw]`

van der Waals energy.

`[elec]`

Electrostatic energy.

`[total]`

Total energy.

Calculate the energy for atoms in `<mask>`

. If no terms are specified, all terms are calculated. Note that the nonbonded energy terms for ’**simple**’ do not take into account periodicity and there is no distance cut-off. Electrostatics can also be determined via the direct sum, Ewald, or particle-mesh Ewald summation procedures. The particle

mesh Ewald functionality requires that CPPTRAJ be compiled with FFTW and a C++11 compliant compiler.

Calculation of energy terms requires that the associated topology file have parameters for any of the calculated terms, so for example angle calculations are not possible when using a PDB file as a topology, etc. All nonbonded calculations methods other than **simple** require unit cell parameters.

For example, to calculate all energy terms and write to a Grace-format file:

parm DPDP.parm7 trajin DPDP.nc energy DPDP out ene.agr