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