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Desmond User's Guide Desmond User’s Guide Desmond Version 2.2 / Document Version 0.3 June 2009 D. E. Shaw Research Notice The Desmond User’s Guide and the information it contains is offered solely for educa‐ tional 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 responsibility 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 informa‐ tion. 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. Copyright © 2009 by D. E. Shaw Research. All rights reserved. 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. June 2009 Preface Intended audience This guide is intended for computational scientists using Desmond to prepare configura‐ tion and structure files for molecular dynamics simulations. It assumes a broad familiarity with the concepts and techniques of molecular dynamics simulation. Prerequisites Desmond runs on Intel™‐based Linux® systems with Pentium™ 4 or more recent proces‐ sors; running CentOS 3 (RHEL3) or later. Linux clusters can be networked with either Ethernet™ or Infiniband®. To build the source code, Desmond requires gcc Version 4.1.2 and glibc Version 2.3. Viparr requires a recent version of Python; we recommend Version 2.5.1. This guide assumes that someone has prepared Desmond executables for you, either by installing a binary release or by building an executable. About this guide This manual contains the following sections: Key Concepts explains the basic ideas underlying Desmond and describes how Desmond fits into a workflow. June 2009 D. E. Shaw Research i Desmond User’s Guide Running explains the basics of working with configuration files; describes how to invoke the var‐ Desmond ious Desmond executables, including in parallel; and describes how to configure the Desmond executables and built‐in plugins, as well as the optional profiling mechanism. The Global Cell discusses Desmond’s parallelization strategies and describes how to configure the global cell. Preparing a describes how Desmond interprets a structure file, and explains how to use the scripts structure file provided to add force field and constraint information to the structure file. Calculating provides a high‐level overview of configuring force fields; then discusses the computa‐ force and tions involved in, and how to configure, the various interactions. It also describes addi‐ energy tional off‐atom interaction sites. Constraints describes the constraints available to eliminate the fastest vibrational motions and how to configure them. Dynamics summarizes the basic concepts of particle dynamics and describes how to configure the migration interval, timestep scheduling, pressure, and temperature. It also describes each of the available dynamical systems, and how to configure them. Free Energy explains the concepts necessary to configure ligand‐binding and alchemical free‐energy Simulations simulations and those using the Bennett acceptance ratio method, as well as describing how to prepare a structure file for free energy simulations. Extending provides practical details for implementing a plugin, describes the C++ base classes Desmond available for you to subclass, and explains how to load your plugin, what happens when it begins execution, and what happens when it stops. Units explains how numbers provided as configuration parameters are interpreted. Configuration describes configuration file syntax. syntax Clone Radius provides the full set of restrictions on the size of the clone radius, for those who need Restrictions more than the practical guidelines given in Chapter 3. References provides bibliographic information for references given in the text. License includes the licensing restrictions for using Desmond and some of its companion soft‐ Information ware. Format conventions Command lines appear in a monospaced font; in some cases, bolding draws your atten‐ tion to a particular part of the command: mdsim --include equil.cfg Placeholders intended to be replaced by actual values are obliqued: mdsim --tpp 4 --restore checkpoint_file Configuration file examples also appear in a monospaced font: mdsim = { title = w last_time = t1 checkpt = { ... } plugins = [ ... ] ii D. E. Shaw Research June 2009 Format conventions ... } 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 monospace font, thus: plugins. When discussed outside of the context of their sections, however, configuration parame‐ ters appear as a keypath, in which the name of each enclosing section appears in order from outermost to innermost, separated by periods. For example, force.non- bonded.far.sigma refers to the sigma configuration parameter in the far subsection of the nonbonded subsection of the force section of the configuration file. About the equations The equations in this document are concerned with scalars, vectors, and matrices of vari‐ ous 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‐dimen‐ sional vector. •A boldfaced lowercase letter, such as a ,is a vector of unspecified dimension, th withai indicating the i element of the vector. •A boldfaced uppercase letter is a matrix of unspecified dimensions, though usually 33× , with Aij being the element of row i and column j in matrix A . Certain quantities that are ‐3n dimensional vectors, such as r , the positions of n particles, are indexed differently. The manual does not use ri to refer to one of its 3n components, th but instead ri denotes the i three‐dimensional vector in r , which is the position of the th i particle in this case. June 2009 D. E. Shaw Research iii Desmond User’s Guide iv D. E. Shaw Research June 2009 Contents Preface i Intended audience . i Prerequisites . i About this guide . i Format conventions. ii About the equations. iii 1. Key Concepts. 1 What is Desmond? . 1 Forces . 2 Particles. 3 Force fields . 4 Space . 4 Time. 5 Dynamics. 5 Using Desmond . 6 Input . 7 Executables and scripts . 7 Output . 7 Workflow. 8 Customizing Desmond . 9 June 2009 D. E. Shaw Research v Desmond User’s Guide 2. Running Desmond . 11 About configuration . 11 Invoking Desmond . 12 Restoring from a checkpoint . 14 Using plugins . 14 Running Desmond in parallel . 16 Configuring Desmond applications . 17 mdsim. 17 minimize . 18 remd. 19 vrun . 21 Naming output files . 22 Configuring the built‐in plugins. 23 anneal . 23 Biasing Force . 24 compute_forces . 27 energy_groups . 27 eneseq . 28 maeff_output . 29 posre_schedule. 29 randomize_velocities . 30 status . 31 trajectory . 31 Configuring optional sections . 32 profile . 32 3. The Global Cell. 35 Parallelization . 35 Configuration . 37 4. Preparing a structure file. 41 Format . 41 Global cell . 43 Particles and pseudoparticles . 43 Force field sections . 44 Adding force field information . 45 Available force fields . 45 Input and output files . 46 Running Viparr . 47 Options to Viparr . 47 Specifying multiple force fields . 48 User‐defined force fields . 49 Adding constraints . 49 Running the build_constraints script . 50 vi D. E. Shaw Research June 2009 5. Calculating force and energy. 51 Configuring force fields . 51 Bonded, pair, and excluded interactions . 54 Stretch terms ..
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