Umbrella Sampling
Introduction
In this tutorial we will learn how one can apply bias potential along a collective variable (CV) and derive a system from one thermodynamic state to another. This technique is known as "Umbrella Sampling". We will cover all the intermediate steps by a series of windows (harmonic potential), at each of which we will perform an MD simulation. One of the reason to introduce this potential is to avoid the sampling of un-desired region of the conformational space. We can combine this method with Weighted Histogram Analysis Method (WHAM) to generate the free energy surface.
The time independent bias potential which is usually taken to be harmonic form is
In this tutorial we will explore the free energy surface of alanine dipeptide in vacuo as a function of two backbone dihedral angles (Φ, Ψ) using umbrella sampling. Here, we are assuming that users are familiar with AMBER and can run MD simulation using PLUMED-AMBER interface. The first thing we need to do is build an initial structure using ff14SB force-field and relax this at 300K so that we can use this as the input. What we do is:
- Minimize (2000 steps)
- Heat (optional for small system)
- Relax (300K, 100ps)
