Constant pH Advanced Options Dialog Box
Set options for the pH range and simulation for constant pH MD simulations.
To open this dialog box: click the Change link in the Protein Constant pH Simulations Panel.
- Using
- Features
- Additional Resources
Using the Constant pH Advanced Options Dialog Box
The pH range should span the expected pKa values, with a margin of 1 – 2 units on either side.
Constant pH Advanced Options Dialog Box Features
- pH Settings section
-
Set up the pH values for the simulation. The pH range should span the expected pKa values, with a margin of 1 – 2 units on either side. The default values are chosen to cover the pH range relevant to the supported titratable residues.
The pH values are set up by starting with the lower limit and adding successive interval values until the upper limit is reached.
- pH lower text box
-
Lower limit of the pH range sampled in the simulation. This value is the starting value for generation of the pH values used in the simulation.
- pH upper text box
-
Upper limit of the pH range sampled in the simulation. The largest pH value generated is less than or equal to this value, depending on whether the pH range (pH upper − pH lower) is an integer multiple of the interval value. If it is not, this value is not included in the generated set.
- pH interval value text
-
Interval used to generate intermediate pH values. The value is added to each pH value to generate the next value, starting with the lower limit. This value cannot be changed.
- Replicas text box
-
Noneditable text box that displays the number of replicas. This number changes as you change the upper and lower pH limit values.
- Simulation Parameters section
-
Set parameters for the MD simulations.
- Simulation time text box
-
Specify the desired simulation time in ps. Longer simulation times can improve the accuracy of the results, at the expense of longer computation time.
- Set random number seed option and text box
-
Select this option to specify a random seed to be used in the simulations. Specifying the seed allows you to reproduce the results, unless other factors affect them. If this option is not selected, a seed is chosen at random.
- Reset button
-
Reset the panel to its default settings.