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Desmond Users Guide Release 3.4.0 / 0.7 Desmond Users Guide Release 3.4.0 / 0.7 D. E. Shaw Research December 18, 2012 CONTENTS 1 Front matter 3 1.1 Notice..................................................3 1.2 Copyright.................................................3 1.3 Trademarks................................................3 2 Preface 5 2.1 Intended audience............................................5 2.2 Prerequisites...............................................5 2.3 Format conventions...........................................5 2.4 About the equations...........................................6 3 Key Concepts 7 3.1 What is Desmond?............................................7 3.2 Forces..................................................8 3.3 Particles.................................................9 3.4 Force fields................................................9 3.5 Space................................................... 10 3.6 Time................................................... 10 3.7 Dynamics................................................. 11 3.8 Using Desmond............................................. 12 4 Running Desmond 15 4.1 About configuration........................................... 15 4.2 Invoking Desmond............................................ 16 4.3 Running Desmond in parallel...................................... 19 4.4 Configuring Desmond applications................................... 20 4.5 Naming output files........................................... 25 4.6 Configuring the built-in plugins..................................... 25 4.7 Configuring optional sections...................................... 37 5 The Global Cell 39 5.1 Parallelization.............................................. 39 5.2 Configuration............................................... 42 5.3 Migration................................................. 43 6 Preparing a structure file 45 6.1 Converting a Desmond 2.0/2.2 structure file............................... 45 6.2 Preparing a Desmond DMS file..................................... 46 7 Calculating Force and Energy 49 i 7.1 Configuring force fields......................................... 49 7.2 Bonded, pair, and excluded interactions................................. 51 7.3 Van der Waals and electrostatic interactions............................... 57 7.4 Nonbonded far interactions....................................... 60 8 Constraints 65 8.1 Single precision resolution and constraints............................... 67 9 Dynamics 69 9.1 Particles and mechanics......................................... 69 9.2 Integrator................................................. 70 9.3 RESPA.................................................. 71 9.4 Pressure.................................................. 72 9.5 Temperature............................................... 73 9.6 Dynamical systems............................................ 73 10 Free Energy Simulations 93 10.1 Configuring free energy simulations................................... 93 11 Enhanced Sampling and Umbrella Sampling 99 11.1 Introduction............................................... 99 11.2 Using the Enhanced Sampling Plugin.................................. 100 11.3 Interpreter................................................ 100 11.4 Metadynamics.............................................. 105 11.5 Examples................................................. 106 12 Extending Desmond 109 12.1 Implementation.............................................. 109 12.2 Running your plugin........................................... 110 13 Trajectory Format and Analysis 111 13.1 Structure of frameset directories..................................... 111 13.2 Soft catenation option.......................................... 112 13.3 Command line tools for framesets.................................... 112 13.4 Python tools for trajectories and framesets............................... 114 14 Appendix: Units 119 15 Appendix: Configuration syntax 121 15.1 Examples................................................. 122 16 Appendix: Clone Radius Restrictions 125 17 Appendix: DMS file format 127 17.1 Molecules................................................ 127 17.2 Forcefields................................................ 129 17.3 Alchemical systems........................................... 131 18 Legacy Applications: Preparing a Maestro structure file 133 18.1 Format.................................................. 133 18.2 Preparing the structure file for Free Energy Simulations........................ 136 19 Enhanced sampling function reference 143 20 Licenses and Third-Party Software 155 20.1 Licensing Desmond for Non-Commercial Research........................... 155 ii 20.2 Licensed Companion Software...................................... 158 Bibliography 163 iii iv Desmond Users Guide, Release 3.4.0 / 0.7 Release 0.6.0 Date December 18, 2012 Contents: CONTENTS 1 Desmond Users Guide, Release 3.4.0 / 0.7 2 CONTENTS CHAPTER ONE FRONT MATTER 1.1 Notice The Desmond User’s Guide and the information it contains is offered solely for educational purposes, as a service to users. It is subject to change without notice, as is the software it describes. D. E. Shaw Research assumes no respon- sibility or liability regarding the correctness or completeness of the information provided herein, nor for damages or loss suffered as a result of actions taken in accordance with said information. No part of this guide may be reproduced, displayed, transmitted, or otherwise copied in any form without written authorization from D. E. Shaw Research. The software described in this guide is copyrighted and licensed by D. E. Shaw Research under separate agreement. This software may be used only according to the terms and conditions of such agreement. 1.2 Copyright 2012 by D. E. Shaw Research. All rights reserved. 1.3 Trademarks Ethernet is a trademark of Xerox Corporation. InfiniBand is a registered trademark of systemI/O Inc. Intel and Pentium are trademarks of Intel Corporation in the U.S. and other countries. Linux is the registered trademark of Linus Torvalds in the U.S. and other countries. All other trademarks are the property of their respective owners. 3 Desmond Users Guide, Release 3.4.0 / 0.7 4 Chapter 1. Front matter CHAPTER TWO PREFACE 2.1 Intended audience This guide is intended for computational scientists using Desmond to prepare configuration and structure files for molecular dynamics simulations. It assumes a broad familiarity with the concepts and techniques of molecular dy- namics simulation. 2.2 Prerequisites Desmond runs on Intel based Linux systems with Pentium 4 or more recent processors; running CentOS 5.4 (RHEL5) or later. Linux clusters can be networked with either Ethernet or InfiniBand. To build the source code, Desmond is known to work with gcc Version 4.5.2 and glibc Version 2.5. Certain python scripts require a recent version of Python 2 (version 3 is not supported); we recommend Version 2.7.1 or greater. This guide assumes that someone has prepared the Desmond executable for you, either by installing a binary release or by building the executable. 2.3 Format conventions Command lines appear in a typewriter font; in some cases, bolding draws your attention to a particular part of the command: $ desmond --include equil.cfg Placeholders intended to be replaced by actual values are obliqued: $ desmond --tpp 4 --restore checkpoint_file Configuration file examples also appear in a typewriter font: mdsim = { title = w last_time = t1 checkpt = { ... } plugin = { ... } } Configuration files are divided into sections, which can in turn contain other sections; parameters occur at all levels. When discussed in the context of their particular section, configuration parameters appear by name in a typewriter font, thus: plugin. When discussed outside of the context of their sections, however, configuration parameters appear as a keypath, in which the name of each enclosing section appears in order from outermost to innermost, separated by 5 Desmond Users Guide, Release 3.4.0 / 0.7 periods. For example, force.nonbonded.far.sigma refers to the sigma configuration parameter in the far subsection of the nonbonded subsection of the force section of the configuration file. 2.4 About the equations The equations in this document are concerned with scalars, vectors, and matrices of various sorts. To help clarify the type of a quantity, equations in this manual use the following conventions: • An upper or lowercase letter without bolding or arrows, such as A or a, is a scalar. • An arrow over a variable, such as A~ or ~a, indicates three variables as a three-dimensional vector. th • A boldfaced lowercase letter, such as a, is a vector of unspecified dimension, with ai indicating the i element of the vector. • A boldfaced uppercase letter, such as A, is a matrix of unspecified dimensions, though usually 3 × 3, with Aij being the element of row i and column j in matrix. Certain quantities that are 3n dimensional vectors, such as r, the positions of n particles, are indexed differently. The th manual does not use ri to refer to one of its 3n components, but instead ~ri denotes the i three-dimensional vector in r, which is the position of the ith particle in this case. 6 Chapter 2. Preface CHAPTER THREE KEY CONCEPTS This chapter explains the basic ideas underlying Desmond and describes how Desmond fits into a workflow. 3.1 What is Desmond? Desmond is a suite of computer programs for carrying out molecular dynamics simulations. Such simulations model the motion of a collection of atoms—a chemical system—over
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