PURPOSE: This protocol is a modified version of the standard "Minimization" protocol. It exposes two new parameters under the Minimization Constraints parameter; Constraint Scale and Scale Frequency Steps. This protocol allows the user to not only add constraints but also scale the constraint force constants by a factor (Constraint Scale) every Scale Frequency Steps of minimization.

This version does not include the Implicit Solvent Model, Electrostatics or Apply SHAKE Constraints options.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in Discovery Studio only, go to the Protocol Explorer, right-click over the folder you want to add the protocol to, choose Import, navigate to the location of the Minimization Scaling Constraints.xml file and enter it as the File Name.

REQUIREMENTS: Discovery Studio Embedded Collection, CHARMm

KEYWORDS: minimization, scaling force constants, constraints

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.1 and Pipeline Pilot Server versions 6.1.6 and 7.0.1 (SES). It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.