Subsections

• Configuration File
• Run your Simulation

Ubiquitin in a Water Box: Simulation with Periodic Boundary Conditions

In this section, you will examine the minimization and equilibration of ubiquitin in a water box with periodic boundary conditions.

Configuration File

1

Go to your 1-3-box directory by typing cd ..$\backslash$1-3-box. Here, you will find a configuration file for the minimization and equilibration of ubiquitin in a water box. All output files for the minimization and equilibration of your ubiquitin in a water box system will be placed in this directory.

2

Open the configuration file, ubq_wb_eq.conf using WordPad.

The configuration file contains some commands which are different than the water sphere configuration file. Here, these differences are pointed out and explained.

3

The only differences in this file lie in the ``Simulation Parameters" section, where three new categories of parameters have been added. The ``Output" section has also been modified. The new commands are listed:

• Periodic Boundary Conditions
  • Three periodic cell basis vectors are to be specified to give the periodic cell its shape and size. They are cellBasisVector1, cellBasisVector2, and cellBasisVector3. In this file, each vector is perpendicular to the other two, as indicated by a single $x$, $y$, or $z$ value being specified by each. For instance, cellBasisVector1 is $x=42$Å, $y=0$Å, $z=0$Å. With each vector perpendicular, a rectangular 3-D box is formed.
  • cellOrigin: specifies the coordinates of the center of the periodic cell in Å. This is why you need to calculate the center of your water box after you solvate!
  • wrapWater: This command may be used with periodic boundary conditions. If a water molecule crosses the periodic boundary, leaving the cell, setting this command to on will translate its coordinates to the mirror point on the opposite side of the cell. Nothing can escape. The command may be set to on or off.
  • wrapAll: same as wrapWater, except this applies to all molecules.
• Electrostatics with PME

  Particle Mesh Ewald (PME) is a useful method for dealing with electrostatic interactions in a system when periodic boundary conditions are present. The Ewald sum is an efficient way of calculating long range forces in a 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. As a result, your grid size should be chosen such that it is fine enough to accurately represent the configuration of your system.

  • PME: indicates whether or not the simulation uses the Particle Mesh Ewald Sum method; uses values yes and no.
  • PMEGridSpacing: sets the minimum ratio between the number of PME grid points along each cellBasisVector and the physical dimensions. Since the grid will replicate the charge distribution in your system, PMEGridSpacing should be chosen to be large enough so that the grid spacing accurately reproduces your charge distribution. However, it should not be so large that it will slow down your simulation to provide unnecessary precision. Typically, a grid density of slightly more than 1/Å is a good choice to reproduce charge distribution in biological systems, where the closest atoms have a bond separation on the order of 1 Å. This corresponds to a PMEGridSpacing of 1.0. NAMD will then automatically set the PME grid sizes (see below) such that there is always less than 1.0 Å between grid points and the sizes contain only small prime factors (e.g. 2, 3, and 5).

  Alternatively, one can define the PME grid sizes manually, using PMEGridSizeX, PMEGridSizeY, and PMEGridSizeZ. These set the size of the PME grid along cellBasisVector1, 2 and 3, respectively (not the $x$, $y$, and $z$ directions as implied). For speed in computing Fast Fourier Transforms, PMEGridSizeX should be chosen so that it can be factorized by 2, 3, or 5. If your cellBasisVector1 = (60, 0, 0), a good choice for PMEGridSizeX might be 64, since 60 Å / 64 = 0.9375 Å and $64=2^{6}$. 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.

• Constant Pressure Control (variable volume)
  • useGroupPressure: NAMD calculates system pressure based on the forces between atoms and their kinetic energies. This command specifies whether interactions involving hydrogen should be counted for all hydrogen atoms or simply between groups of hydrogen atoms; uses values yes and no and must be set to yes if rigidBonds are set.
  • useFlexibleCell: specifies whether or not you want to allow the three dimensions of the periodic cell to vary independently; uses values yes or no.
  • useConstantArea: NAMD allows you to keep the $x-y$ cross sectional area constant while varying the $z$ dimension; uses values yes and no.
  • langevinPiston: indicates whether or not the simulation uses a Langevin piston to control the system pressure; uses values on and off.
  • langevinPistonTarget: specifies, in units of bar, the pressure which the Langevin piston tries to maintain. (1 atm = 1.013 bar)

    The following are specifications for the Langevin piston which NAMD allows you to specify.

  • langevinPistonPeriod: sets the oscillation time constant in fs for the Langevin piston.
  • langevinPistonDecay: sets the damping time constant in fs for the Langevin piston.
  • langevinPistonTemp: sets the ``noise" temperature in K for the Langevin piston; should be set equal to the target temperature for the temperature control method (here, set by langevinTemp).
• Output
  • xstFreq: The extended system trajectory file contains a record of the periodic cell parameters, essentially recording the trajectory of the cell boundaries over the run time. This command specifies how often, in time steps, the configuration will be recorded. If this command is set, three xst files will be output: 1 final and 2 restarts.
  • outputPressure: specifies the number of time steps between each output of system pressure into the .log file.

Note that the commands which specify spherical boundary conditions have been completely removed, since this simulation is using periodic boundary conditions.

Run your Simulation