Energy and relevant terms reported by Modar
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Modar reports energies profiles and relevant terms both in log file and in binary format “.ene” file (see previous section), here is the list of abbreviations used in Modar, the units measurement please see §8
Abbreviation
Description
Function form
in most of force fieldsMD Time
MD simulation time in pico-second
Bond
Bond strength energy
Angle
Angle strength energy
Urey
Urey-Bradley, the strength energy between 1-3 atoms of angles in CHARMM force field
Dihedral
Dihedral torsion energy
ImprDihe
Improper Dihedral bending energy
Cmap
Cross terms for the main chain of peptide in CHARMM force field
in 2D cubic spline inteplotion
Ele
The electrostatic energy in short range
VdW
The VdW energy
Ele14
The electrostatic energy from 1-4 atoms interaction in dihedrals
The same as Ele but with a scale factor
VdW14
The VdW energy from 1-4 atoms interaction in dihedrals
The same as VdW but with a scale factor
NBtot
Summation of electrostatic and VdW energy in short range only
EwExcl
The bonds corrected energy for Ewald
see §5.4.2.
EwKsum
The long range electrostatic by Ewald summation
EwSelf
The self corrected terms for Ewald
Potential
Total potential energy
Temperature
Instant temperature derived from kinetic energy
See §5.6.1.
PressureI
Pressure calculated from internal viral
See §5.6.5.
VirialI
Internal viral
Volume
Volume of MD system with PBC
Density
In g/cm3
PistonPE
The potential energy of virtual particles for NPT coupling
PistonKE
The kinetic energy of virtual particles for NPT coupling
SurfT
Surface tension of xy plane
Kinetic
Kinetic energy
SteeredW
The work of steered MD
See §3.52
SteeredF
The force of steered MD
ExEFE
The energy exerted by the external electric field
See §3.2
RestraintEi
The total energy contributed by the internal constraints
RestraintEe
The total energy contributed by the external constraints
QM
The energy from QM part
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