Colvars question

Hi all,

I'm doing a 1D ABF calculation and my reaction coordinate is Z direction of the cartesian system. But in order to limit the simulation in x and y directions I'm defining two other reaction coordinates, x and y. The sole application of these two reaction coordinates are for using their "lowerWall" and "upperWall" options to enforce the molecule remains in the desired window in x and y directions but I'm not using them in free energy calculation part of abf, i.e. just using "colvars z" in the abf part of the config file. I was wondering if this is a right way of confining the molecule in the directions that I'm not doing free energy calculations?


Yes, it is.