Dear Lammps users:
I am trying to calculate the PMF of a Na+ above the crystal layer. But I am confused about the command “fix smd”, I don’t understand exactly “the equilibrium distance of the spring” and “accumulated PMF (the sum of pulling forces times displacement)” mean.
Isn’t that “the equilibrium distance of the spring” equal to R0 ?
no. R0 is a term that fix smd has inherited from fix spring. it should be set to 0.0 for almost any use case.
And “accumulated PMF” is the final value “potential of mean force” ?
And can I use “umbrella sampling” in lammps directly or need other software ?
it should be possible with fix spring.
in general for these kind of applications I would recommend to use either the fix colvars from the USER-COLVARS package or fix plumed from the USER-PLUMED package. both fixes are part of packages that have a detailed and good documentation outside of LAMMPS, tutorials and are compatible with multiple MD packages and are in many ways far more sophisticated and flexible than what fix smd and fix spring offer.
Axel.