Simulation Output

This page documents all of the primary output files produced by the pipeline and by LAMMPS during and after the simulation. Each subsection shows a representative excerpt (or header) from the file, followed by a line-by-line explanation of its contents. No analysis is performed here—just plain descriptions of what each column or section means.

Thermodynamic Data: Thermo_<fName>.dat

Below is the header line and the first few rows of a typical thermodynamic output file:

# Steps Temp KinEng PotEng Epair Ebond Eangle Bonds
1000000 309.9092980089979 12932.006720561228 2421.2753602970483 -5608.9113003346756 -1676.5739699962255 9706.7606306279486 14845
2000000 308.4459769650038 12870.944733402906 580.1671941493225 -6212.513108889987 -2765.9452470589113 9558.625550098221 15019
3000000 308.9000673416380 12889.893180061661 -663.6937637213039 -6715.222056123977 -3378.1828104342594 9429.711102836933 15138
4000000 307.9393191012913 12849.802731724838 -1247.4935140060538 -7047.389388496154 -3702.186514574762 9502.082389064863 15199

Explanation

  1. Header

    # Steps Temp KinEng PotEng Epair Ebond Eangle Bonds

    • Steps – Current LAMMPS timestep.

    • Temp – Instantaneous temperature (K).

    • KinEng – Total kinetic energy (kcal mol⁻¹).

    • PotEng – Total potential energy.

    • Epair – Pairwise (non-bonded) energy.

    • Ebond – Bond energy.

    • Eangle – Angle energy.

    • Bonds – Total number of bonds at that step.

  2. First data row (for example 1000000 309.909… 12932.0067 …) follows the same column order.

Bond-Formation/Breaking Data: BondData_<fName>.dat

Snippet:

1000000 1566 521
2000000 2417 1198
3000000 3330 1992
4000000 4191 2792

Columns

  • Step – Timestep of the record.

  • Cumulative Bonds Formed – Total new bonds so far.

  • Cumulative Bonds Broken – Total breaks so far.

Collective-Variable Trajectory: <fName>.colvars.traj

# step         Rg1
       0    2.76034911120119e+02
   50000    2.74510753203738e+02
  100000    2.73564239569613e+02
  150000    2.73851073534982e+02

  • step – LAMMPS timestep.

  • Rg1 – Radius of gyration (Å).

LAMMPS Dump Trajectory: traj_<fName>.dump

Each block begins with ITEM: TIMESTEP and ends with an ATOMS table:

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
14000
ITEM: BOX BOUNDS pp pp pp
-4.20e+02 4.20e+02
-4.20e+02 4.20e+02
-4.20e+02 4.20e+02
ITEM: ATOMS id type mol mass x y z xu yu zu
10550 4 151 1000 -184.08 -109.786 -288.422 -184.08 -109.786 -288.422
…

Key columns are id, type, mol, mass, wrapped (x y z) and unwrapped (xu yu zu) coordinates.

Colvars Metadynamics Hills: <fName>.colvars.meta-radgy.hills.traj

   0     2.65169992360953e+02    1.00000000000000e+00   2.00000000000000e-01
 500     2.65195448031953e+02    1.00000000000000e+00   2.00000000000000e-01
1000     2.65215417786256e+02    1.00000000000000e+00   2.00000000000000e-01

Columns: index (colvar steps), R<sub>g</sub>, hill height, hill width.

Potential of Mean Force (PMF): <fName>.pmf

# 1
#          0         1       277  0
 0.5  1711.9
 1.5  1711.9
 2.5  1711.9

  • First column – Bin centre (Å).

  • Second column – PMF value (kcal mol⁻¹).

Restart Files

Intermediate restarts (<fName>_tp_*.restart)

Binary snapshots written every dt_restart steps let you resume from an earlier point:

lmp_serial -r <fName>_tp_25000000.restart -in <restart_input.in>

Final restart (final_state_<fName>.restart)

Written at the end of the production run; useful for visualisation or as the starting point for a new simulation.

LAMMPS Log File: <fName>.log

Captures start-up messages, warnings/errors and (optionally) thermo output. A typical header:

LAMMPS (5Dec20)
Reading data file ...
  orthogonal box = (-420 420) x (-420 420) y (-420 420) z
  14000 atoms
  13800 bonds
  13600 angles

Summary of All Simulation Outputs

  • ``Thermo_<fName>.dat`` – step, temperature, energies & bond count.

  • ``BondData_<fName>.dat`` – cumulative bonds formed/broken.

  • ``<fName>.colvars.traj`` – colvar history.

  • ``traj_<fName>.dump`` – full atom snapshots.

  • ``<fName>.colvars.meta-radgy.hills.traj`` – metadynamics hills.

  • ``<fName>.pmf`` – final PMF vs colvar.

  • ``<fName>_tp_*.restart`` – periodic binary restarts.

  • ``final_state_<fName>.restart`` – last restart in the run.

  • ``<fName>.log`` – LAMMPS log (setup, warnings, optional thermo).