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Minimize - Options Dialog Box |
In the Minimize - Options dialog box you can select options for minimization of a protein structure, including use of an implicit membrane and crystal symmetry, the solvent dielectric constant, algorithm selection, and convergence criteria.
To open the Minimize - Options dialog box, you can:
Click Options in the Minimize panel.
These options allow you to specify the environment of the protein, other than the use of an implicit solvent.
Use the environment specified in the main panel, which could be a vacuum or an implicit solvent.
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. Conversely, hydrophilic groups lose any short-ranged solvation energy from the high dielectric region when moving into 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.
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.
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.
Choose the minimization method, from Quasi-Newton (LFBGS), Truncated Newton, Conjugate gradient, and Automatic. The Automatic method uses conjugate gradient minimization when the gradients are large, and switches to the truncated Newton method when they are sufficiently small.
Specify the number of iterations to be performed for the minimization. At the beginning of each iteration, various updates are performed, such as on solvent parameters and long-range pairs. Iterating reduces the accumulation of errors in the minimization. The minimization stops if the specified number of iterations is completed.
Specify the maximum number of steps to take in each minimization iteration. Each step involves one application of the chosen algorithm to obtain a new geometry. The iteration cycle finishes when the maximum number of steps is completed.
Specify the RMS gradient threshold for convergence of the minimization, in kcal mol-1 Å-1. The minimization stops if the RMS gradient is smaller than the specified value.
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