AMBER TI Tutorials

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A simple TIMD tutorial about T4-lysozyme

Introduction to TIMD

This is a TIMD tutorial based on the tutorial written by Thomas Steinbrecher on the site[1]. But some important changes have been made to suit the current AMBER 10 version according to Miranda's tutorial from Simmerling's lab[2].

In this tutorial, free energy calculations will be used to calculate the relative binding free energy of two simple ligands, benzene and phenol to the T4-lysozyme mutant L99A. Free energies will be computed by using the thermodynamic integration facilities of the sander program. A modified van-der-Waals equation (softcore potentials) are used to ensure smooth free energy curves.

Thermodynamic cycle and Method

TI calculations compute the free energy difference between two states A and B by coupling them via a parameters λ that serves as an additional, nonspatial coordinate. This λ formalism allows the free energy difference between the states to be computed as:

Setup of the T4 System

Generate Start Structures

Setup and run MD