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

• Overview

• Installing on Linux

• Installing on Windows (experimental version)

• Setting xTB

Interface basics

• Interface overview

• Importing a new system

• Selections

• Selection lists and restraints

• Harmonic restraints

• Colors and representations

• Cartoon representation

• Molecular surfaces

• Fixing atoms

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

• Charge corrections

• Trajectory handler

• Importing/exporting data

• Interface themes and fog

• AI control and assistants (Claude Code, local models)

Simulations

• Single points and energy refinement

• Geometry optimizations

• Molecular dynamics

• Normal modes

• Reaction coordinate scans

• Advanced reaction coordinate scans

• Umbrella Sampling

• Nudged elastic band (NEB)

• Conjugate Peak Refinement (CPR)

• Transition state search (Baker)

• IRC / Reaction path

• Excited states (MNDO-CI / MOM)

• Remote machines (ssh, SLURM)

Analysis

• Trajectory Alignment

• Reimaging (Wrapping)

• Distance, Angle, and Dihedrals

• RMSD Tool

• RMSF Analysis

• RDF Analysis (g(r))

• Box Density Analysis

• Ramachandran Plot

• Trajectory Analysis (DSSP, SASA, H-bonds, PCA, clustering...)

• Potential energy landscape analysis (PES Analysis)

• Normal modes and IR spectra

• Weighted Histogram Analysis Method (WHAM)

• Umbrella Sampling Browser

• Orbitals and Surfaces

• Molecular Properties (symmetry, CIP, ion mobility)

• Cavities and Pockets

Miscellaneous

• Hybrid QC/MM potentials

• QC/MM and Charge Rescaling

• Charges: Block Inspector, fragment-based, ESP and RESP

• Force field tools (OPLS, DYFF, parameters)

• DYFF manual

• Solvation and system operations

• Cell and Symmetry