energy

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

energy [<name>] [<mask1>] [out <filename>] [nobondstoh] 
   [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.
[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