MBO(N)D

Contents

Release 2000, March 2000


Table of Contents i

1. Introduction

What Is MBO(N)D?

MBO(N)D--The Insight and standalone modes of operation

Starting MBO(N)D

Using this guide

Additional information

Notes on command names

2. Theory and Implementation

The MBO(N)D approach

Multigranularity

Computational speedups

Substructured molecular dynamics

Multibody dynamics

Substructuring the macromolecular model

Generating component modes for flexible bodies

System modes versus component modes

Temperature

Precautions

How temperature is controlled

Constraints during dynamics simulations

Integration algorithms

Brief description of the MBOND/CHARMm interface

3. General Methodology

Substructuring strategies

Molecular domains

Alpha helices and pseudodihedral angle analysis

Beta sheets and interpeptide plane angle analysis

Loops and turns

Sidechain substructuring

Lessons learned

Other analytical methods to aid substructuring

Analysis of B-factor data

Difference between two experimental conformations

Secondary structure calculation

Substructured dynamics and topological loops

Choice of reference coordinates and selection of modes

Initial coordinates and velocities

Stages and duration of dynamics simulation

Dynamics output

4. Methodology--Insight

Preliminary tasks

Preparing the model

Minimizing the model

Substructuring

Example 1

Example 2

Example 3

Generating modes

Loading modes

Animating modes

Setting up the MBO(N)D simulation run

Specifying how to handle nonbond interactions

The Miscellaneous Mean Field Potential (MMFP)

Constant VELocity method (CVEL)

Setting up the dynamics calculation

Constant-temperature dynamics, equilibration stage

Constant-temperature dynamics, atomistic data-collection stage

Constant-energy dynamics, data collection

Output frequencies

Stream files

Setting up the parameter mode

MTS integrator

Setting up the background job

Running the MBO(N)D simulation

Submitting the MBO(N)D job

Monitoring a background job

5. Command Summary--Insight

Bodies pulldown

Modes pulldown

SetUp pulldown

MBOND_Run pulldown

Background_Job pulldown

6. Command Summary--Standalone Mode

MBO(N)D-specific keywords

MBO(N)D dynamics keywords

7. Methodology--Standalone Mode

Running an MBO(N)D simulation in standalone mode

Input files required

General MBO(N)D procedure

General outline of command input file

Specific commands

8. Tutorials

Introduction and overview of Pilot online tutorials

A. References

B. File Formats

Input files

MBO(N)D-specific files

C. Miscellaneous

Technical notes

Unsupported CHARMm facilities

D. Commands--Standalone Mode

Documentation format

CHARMm command lines

General format of MBO(N)D as single-line command

General format of MBO(N)D command block

Detailed command descriptions

CVEL

DYNAMICS

GENERATE

MBOND

MODES

MTS integrator

SUBStructure Index 93