In this section, you will examine the minimization and equilibration of ubiquitin in a water box with periodic boundary conditions.
The configuration file contains some commands which are different than the water sphere configuration file. Here, these differences are pointed out and explained.
PME stands for Particle Mesh Ewald Sum, and is useful in dealing with potentials in the system when periodic boundary conditions are present. The Ewald sum is an efficient way of calculating long range forces in the periodic system. The particle mesh is a 3-D grid created in the system over which the system charge is distributed. From this charge, potentials and forces on atoms in the system are determined.
Note that since cellBasisVector is defined with slightly different values in each direction, the size of the mesh spacing (in length) will be different in each direction.
Note also that when using the PME method, the command cutoff dictates the separation between long and short range forces for the method; it does not simply turn off interactions.
The following are specifications for the Langevin piston which NAMD allows you to specify.
Note that the commands which specify spherical boundary conditions have been completely removed, since this simulation is using periodic boundary conditions.