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

his is place for pDynamo users to cooperate and exchange information and experiment with new ideas. As such, much of the material here is neither guaranteed nor meant to be completely bug-free, user-friendly and fool proof. Please get in touch with the wiki administrator if you wish to contribute.

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

  • QC/MM and Charge Rescaling