Energy Files

Desmond Energy (.ene) files contain information on various energies at each time step of a simulation. The ene file is a plain text file, predominantly consisting of a table of energies (and other summary data) reported at each requested timestep. After the table header, each row corresponds to a timestep, and values are separated by whitespace. The top of the ene file includes commented out lines (starting with #) which include some potentially helpful extra information about the system. This includes the number of particles (N atoms), the number of degrees of freedom (N dof), the total charge (sum_i q_i) as well as the total squared charge (sum_i q_i^2). Additional information may be included depending on the simulation configuration. See the below table for the various headers that might be contained in an .ene file, and what they correspond to.

E	Conserved energy – this corresponds to the sum of potential, kinetic, and extended system energy. For many integration methods, this quantity is asymptotically conserved as the simulation timestep goes to ∞ and serves as a check on the correctness of the trajectory.
E_p	Potential energy at the given timestep
E_k	Kinetic energy at the given timestep
E_x	Extended energy – this is the energy associated with the extended variables of the dynamical system being integrated
E_c	The center of mass kinetic energy of the entire system. If no steps are taken to periodically remove center of mass motion (i.e. setting the remove_com_motion parameter), this quantity can grow over time.
E_f	The force correction value, proportional to the sum of the individual particle forces. This quantity can be of interest as it defines a conserved quantity when added to the energy in certain systems (generally those with velocity Verlet integrators).
P	The system pressure
V	The system volume
T	The system temperature

Ene files are also the input to the Simulation Quality Analysis Panel, which can visualize thermodynamic properties of the system as a function of simulation time.

See the Examples tab for an example .ene file.

# 7.9.008
# Desmond MD simulation
# Simulation started on Thu Mar 28 14:57:25 2024

# sum_i q_i = -0.000000, sum_i q_i^2 = 407.081369
# N atoms = 1251
# N dof =  2535 ( 2538 )
# N groups = 431

#    0:time (ps)  1:E   (kcal/mol)  2:E_p (kcal/mol)  3:E_k (kcal/mol)  4:E_c (kcal/mol)  5:E_x (kcal/mol)  6:E_f (kcal/mol)  7:P   (bar)  8:V   (A^3)  9:T     (K)
          0.0000   -3.52034027e+03   -4.21647782e+03    7.29202573e+02    2.79030522e-11   -3.30650216e+01   -6.13416622e+01    -1498.552    14275.324      289.506
          1.2000   -4.23996697e+03   -5.32090747e+03    4.72814485e+01    1.34432915e-02    1.03365905e+03   -9.42017748e+01      527.820    12400.868       18.772
          2.4000   -5.30364285e+03   -5.34829813e+03    3.08072021e+01    9.88752887e-02    1.38480794e+01   -9.48870511e+01      189.212    12329.847       12.231
          3.6000   -5.34708321e+03   -5.36591395e+03    3.40304124e+01    2.46242637e-01   -1.51996685e+01   -9.54330767e+01      -52.784    12418.736       13.511