Cerius²·Forcefield Engines


Release 4.5, June 2000


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
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
Atom types
Diagonal van der Waals
Atom typing rules
Off-diagonal van der Waals
Bond stretch
Angle bend
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


Last updated 10 September 1998.
Copyright © 1997, 1998 Molecular Simulations Inc. All rights reserved.