constrained optimization

If you’re interested in just nailing the positions of the two atoms you could try fixing the velocity of the carbon atoms to zero (with “fix move”) and then, with a “fix viscus”, run dynamics until all the kinetic energy has been dissipated from the system.

Like is says in the minimization portion of the manual ( (
“Or dynamics can be run using fix viscous to impose a damping force that slowly drains all kinetic energy from the system.”

But with the velocity of the atoms you want nailed in place set to zero with the “fix move” command.

Ben Jensen
PhD Student
Michigan Technological University
Mechanical Engineering - Engineering Mechanics
Houghton, MI