Cerius²·Forcefield Engines

Contents

Release 4.5, June 2000

Contents

1. Introduction

Who should use this guide

Other Cerius2 documentation sets

Additional information sources

Typographical conventions

2. Preparing the System

Choosing a forcefield

Specifying automated forcefield loading and setup

Manually loading a forcefield

The CFF forcefield

Loading the MMFF94 or MMFF94S forcefield

Preparing the system

Manually assigning forcefield atom types

Manually assigning bond types

Assigning charges

Setting constraints and restraints

Preparing the energy expression

Handling nonbond interactions

Other energy-expression terms

Manually setting up the energy expression

3. Minimization

Setting up the calculation

Minimization algorithm

Pressure and stress in periodic systems

Termination criteria

Convergence criteria

Maximum number of iterations

Specifying output

Performing a calculation

Minimization

Current energy

4. Dynamics Simulation

Setting up the calculation

Dynamics conditions--the thermodynamics ensemble

Temperature control

Pressure and stress control

Periodic tasks

Timestep and duration of run

Specifying output

Performing a calculation

Simple dynamics runs

Equilibration stage

Data-collection stage

Continuing or restarting interrupted or incomplete runs

Restarting dynamics runs from saved trajectory files

5. Analyzing Results

Preparing trajectories

Loading or creating a trajectory

Selecting frames from a loaded trajectory

Output from analysis

Displaying model conformations

Output as graphs and text

Output in tables format

Property statistics

Basic statistics of various properties

Mean-square displacement

Self-diffusion constant

Velocity autocorrelation

Power spectrum

Radial distribution function

Structure factor

Dipole-dipole interactions

Fluctuation analysis

A. References

B. The Forcefield Editor

Loading and saving forcefield files

Creating and editing atom types and rules

Creating and editing atom types

Creating and editing atom typing rules

Manipulating energy functions and parameters

Editing energy functions and parameters

Changing UFF's generator parameters

C. File Formats

Files documented at our website

Forcefield parameter files

Version number and product name

Header information

Preferences

Atom types

Diagonal van der Waals

Atom typing rules

Off-diagonal van der Waals

Bond stretch

Angle bend

Torsions

Inversions

Urey-Bradley

Hydrogen bonds

Universal forcefield parameter generator

Stretch-bend-stretch cross terms

Stretch-stretch cross terms

Default preferences for Dreiding and Universal forcefields

Pf forcefield parameter file converter

Trajectory files

Index