UFED

Introduction

The aim of this tutorial is to run a Unified Free Energy Dynamics (UFED) simulation using the OpenMM-UFEDMM interface. We will set up a simple simulation of alanine tripeptide in vacuum, analyze the output and estimate free energies from the simulation. The basic form of Lagrangian used in this method is:

Here metadynamics bias is added along auxiliary space variables.

In this tutorial, we will compute the free energy surface of alanine tripeptide in vacuo as a function of four backbone dihedral angles (Φ1, Ψ1, Φ2, Ψ2) using UFED and well tempered metadynamics bias is applied on auxiliary (Φ1, Φ2) CVs . It is modelled using the ff14SB all-atom AMBER force field, and the simulations will be carried out OpenMM-UFEDMM interface.

Reweighting of UFED

The free energy surface F(s) as a function of auxiliary variables at temperature T is constructed from the reweighted probability distribution of the auxiliary variables temperature from a UFED trajectory using

The probability distribution shown in the above equation is computed from the normalized histogram obtained using the trajectory of the auxiliary variables following,

where,

UFED Simulation Files

We need python script and pdb file to run the simulations. The files are given as follows

Page updated

Google Sites

Report abuse