Hybrid Monte Carlo - Options Dialog Box

Hybrid Monte Carlo - Options Dialog Box Features

• Environment options
• Seed options
• Dielectric text box
• Number of steps text box
• Temperature text box
• Ouptut options section

 

Environment options

These options allow you to specify the environment of the protein, other than the use of an implicit solvent.

Default option

Use the environment specified in the main panel, which could be a vacuum or an implicit solvent.

Implicit membrane option and Set Up Membrane button

This option embeds the protein in an implicit membrane. The membrane is a low-dielectric slab that simulates the hydrophobic interior of a membrane. The membrane region is treated in the same way as the high-dielectric implicit solvent region. Hydrophobic groups, which normally pay a solvation penalty for creating their hydrophobic pocket in the high dielectric region, do not have to pay that penalty while in the membrane slab. Hydrophilic groups lose any short-ranged solvation energy from the high dielectric region when placed in the low dielectric region.

The option itself does not add a membrane. To run a refinement with a membrane, you must either add it in the Prime Membrane Setup Panel, or select a project entry for refinement that already has a membrane. To set up the membrane, click Set Up Membrane button. In the Prime Membrane Setup Panel you can set the membrane parameters, and place and adjust the membrane. The membrane parameters are stored with the project entry, so you do not need to set up the membrane if the entry already has one.

Crystallographic unit cell option

If crystal symmetry is known for this protein, apply periodic boundary conditions so that the crystal symmetry is satisfied. The protein is refined in the presence of its crystallographic neigbors.

Seed options

Specify the seed for the random-number generator used in the Monte Carlo procedure.
Random: use a random seed.
Constant: use the integer given in the text box as the seed.

Dielectric text box

Set the dielectric constant for the (continuum) solvent. Note that the solvation models also use a radius parameter, so changing the dielectric constant on its own is not the same as changing the solvent model, unless the radius of the desired solvent is similar to that of the solvent model. The default value is for water.

Number of steps text box

Specify the number of steps to take in the sampling procedure. Each step consists of a short, high-temperature MD simulation followed by a minimization.

Temperature text box

Set the temperature for the MD simulations. The temperature should be high enough to allow exploration of new conformations, but not so high as to allow larger changes such as interconversion of chiral centers.

Ouptut options section

Choose an option for the selection of structures to return.

• Return the lowest energy structures—Return the structures that have the lowest energy, selected from the results of each minimization. The number of structures is set in the Number of structures text box. This is the default option, and the default number of structures is 1.

• Return the final structures from each step—Return the final structure from each step in the sampling, which represents a trajectory for the Monte Carlo sampling. This is a way of checking the course of the sampling for convergence, for example.