User Guide

This guide aims to demonstrate the primary functionalities of the EasyHybrid interface and provide an understanding of how they work.

Installation and setup

• Installing on Linux

• Installing on Windows

• Setting xTB

Interface basics

• • Interface overview

  • Importing a new system

  • Selections

  • Selection lists and restraints

  • Harmonic restraints

  • Colors and representations

  • Fixing atoms

  • Quantum chemistry  (QC) and Hybrid Systems (QC/MM) 

  • Charge corrections

  • Trajectory handler

  • Importing/exporting data

Simulations

• • Single points and energy refinement

  • Geometry optimizations

  • Molecular dynamics

  • Normal modes

  • Reaction coordinate scans

  • Umbrella Sampling 

  • Nudged elastic band (NEB)

Analysis

• • Trajectory Alignment 

  • Reimaging (Wrapping)

  • Distance, Angle, and Dihedrals

  • RMSD Tool

  • Potential energy landscape analysis

  • Normal modes

  • Weighted Histogram Analysis Method (WHAM)

  • Surfaces

Miscellaneous

• • Hybrid QC/MM potentials