Skip to content

addmol.bgf file — On-the-fly molecule insertion (GCMD)

The addmol.bgf file is an optional input that allows ReaxFF to insert molecules during an MD simulation at user-defined intervals.

This enables a Grand-Canonical Molecular Dynamics (GCMD)–like workflow, where molecules are periodically added with controlled temperature or velocity, typically at random locations in the simulation box.

Purpose of addmol.bgf

Using addmol.bgf, ReaxFF can:

  • Insert molecules during an ongoing MD simulation
  • Control insertion frequency
  • Specify initial velocities or temperatures
  • Enforce minimum distance constraints to avoid overlaps
  • Perform gas–surface interaction or adsorption simulations

During execution, ReaxFF prints diagnostic messages to the terminal describing molecule placement attempts and outcomes.

Example 2.13: addmol.bgf file (O₂ insertion)

The following example inserts an O₂ molecule every 1000 MD steps at 250 K, at a random position in the simulation box.

BIOGRF 200
DESCRP O2

FREQADD 1000
VELADD 1

STARTX -9000.0
STARTY -9000.0
STARTZ -9000.0

ADDIST 3.0
NATTEMPT 050
TADDMOL 250.0

FORMAT ATOM
(a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)

HETATM 1 O 0.00000 0.00000 0.00000 O 1 3 0.00000
HETATM 2 O 1.24500 0.00000 0.00000 O 1 3 0.00000

END

Keyword reference

FREQADD

Insertion frequency (in MD iterations).

  • The first insertion always occurs at iteration 5
  • Subsequent insertions occur every FREQADD steps

Example - FREQADD 1000 → insert at 5, 1000, 2000, 3000, ...

VELADD

Controls how initial velocities are assigned.

Value Meaning
1 Assign random velocities based on TADDMOL
2 Read velocities from addmol.vel

STARTX, STARTY, STARTZ

Coordinates of the center of mass of the inserted molecule.

  • If value < -5000.0 → random position
  • Otherwise → fixed position

ADDIST

Minimum allowed distance (Å) between the inserted molecule and existing atoms.

Used to prevent atomic overlap during insertion.

NATTEMPT

Maximum number of placement attempts.

If no valid position is found after NATTEMPT tries (respecting ADDIST), the insertion is skipped.

TADDMOL

Temperature (K) of the inserted molecule.

  • Only used when VELADD = 1
  • Ignored when velocities are read from addmol.vel

Molecule definition

The molecular structure is defined using standard .bgf atom records:

  • FORMAT ATOM lines describe the expected atom record layout
  • HETATM lines define atomic positions and types
  • CONECT records are not required
  • Geometry is inserted as a rigid molecule at placement

Example 2.14: addmol.vel file

When VELADD = 2, velocities are read from a separate addmol.vel file.

This file has the same format as velocity sections in the vels restart file.

Atom velocities (Angstrom/s):

0.676920600871422E+13  0.250389491659681E+13   0.385204179579294E+03
0.638733784812228E+13  0.125025292253893E+13  -0.372288199177400E+03

Each line corresponds to the velocity vector of one atom in the inserted molecule.

Output behavior

  • ReaxFF writes placement diagnostics to the terminal
  • Failed placement attempts and skipped insertions are reported
  • Successful insertions are reflected in trajectory and energy outputs

Typical use cases

  • Gas-phase molecule injection
  • Surface adsorption studies
  • Reactive flux simulations
  • Modeling open-system environments

The addmol.bgf mechanism provides a flexible and powerful way to extend ReaxFF MD simulations beyond fixed-particle ensembles.