# energy

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

energy [<name>] [<mask1>] [out <filename>] [bond] [angle] [dihedral] [nb14] {[nonbond] | [elec] [vdw]} [ etype {simple | directsum [npoints <N>] | ewald [cut <cutoff>] [dsumtol <dtol>] [rsumtol <rtol>] [ewcoeff <coeff>] [skinnb <skinnb>] [mlimits <X>,<Y>,<Z>]} ]

`[<name>`

] Data set name.

`[<mask1>]`

Mask of atoms to calculate energy for.

`[out <filename>]`

File to write results to.

`[bond]`

Calculate bond energy.

`[angle]`

Calculate angle energy.

`[dihedral]`

Calculate dihedral energy.

`[nb14]`

Calculate nonbonded 1-4 energy.

`[nonbond]`

Calculate nonbonded energy (electrostatics and van der Waals).

`[elec]`

Calculate electrostatic energy.

`[vdw]`

Calculate van der Waals energy.

`[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.

`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.

**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