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