This is the input file from lammps example for insertion / deletion of a hexane molecule in ethanol. Could anyone please explain what is V_q1, V_q2 and V_q3 and the script marked bold

LAMMPS LAMMPS General Discussion
1

echo screen
units real
atom_style full

pair_style hybrid lj/class2/coul/long 9.5 lj/class2/coul/long/soft 2 0.5 0.5 9.5
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
pair_modify mix sixthpower tail yes
special_bonds lj/coul 0 0 1

read_data data.init_conf_with_heptane

pair_coeff 1 6 lj/class2/coul/long/soft 0.054 4.01 0.0
pair_coeff 2 6 lj/class2/coul/long/soft 0.054 4.01 0.0
pair_coeff 3 6 lj/class2/coul/long/soft 0.10615754 3.80912744 0.0
pair_coeff 4 6 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
pair_coeff 5 6 lj/class2/coul/long/soft 0.00108740 3.57275476 0.0

pair_coeff 1 7 lj/class2/coul/long/soft 0.054 4.01 0.0
pair_coeff 2 7 lj/class2/coul/long/soft 0.054 4.01 0.0
pair_coeff 3 7 lj/class2/coul/long/soft 0.10615754 3.80912744 0.0
pair_coeff 4 7 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
pair_coeff 5 7 lj/class2/coul/long/soft 0.00108740 3.57275476 0.0

pair_coeff 1 8 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
pair_coeff 2 8 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0
pair_coeff 3 8 lj/class2/coul/long/soft 0.06151694 3.31892497 0.0
pair_coeff 4 8 lj/class2/coul/long/soft 0.02 2.995 0.0
pair_coeff 5 8 lj/class2/coul/long/soft 0.00158519 2.66932028 0.0

timestep 1.0
kspace_style pppm 1.0e-5

**variable lambda equal ramp(0.0,1.0)
**variable q1 equal -0.1590v_lambda
**variable q2 equal -0.1060v_lambda
**variable q3 equal 0.0530*v_lambda

**fix ADAPT all adapt/fep 10 &
** pair lj/class2/coul/long/soft lambda 15 68 v_lambda &
** atom charge 6 v_q1 &
** atom charge 7 v_q2 &
** atom charge 8 v_q3 &
** after yes

thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
thermo_modify line one
thermo 100

fix 1 all nvt temp 300 300 100
run 100000

2

You have defined a variable, let’s say lambda: variable lambda equal ramp(0.0,1.0). To actually use it later in the script you refer to it as v_lambda, which you see here for example: variable q1 equal -0.1590*v_lambda. The same logic applies to v_q1, v_q2 and v_q3.

3

This is a simple example of the use of adapt/fep fix. The manual page from the adapt fix from which it is derived contains a more detailed explanation of what is happening. You can have a look at both to understand how the q variables are used in this simulation.

Concerning the variables, have a look at the variable manual page. The outputs from the ramp command are detailed there.

The examples are there to illustrate the concept and usage described in the manual. It is a good practice to look there first for that kind of questions.