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Desmond User's Guide Desmond User’s Guide Desmond Version 3.0 /Document Version 0.5.3 D. E. Shaw Research 1 April 2011 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 regard- ing 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. Copyright 2011 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 coun- tries. 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. Preface Intended audience This guide is intended for computational scientists using Desmond to prepare config- uration 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 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 4.5.1 and glibc Version 2.5. Certain python scripts require a recent version of Python; 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. Preliminary support is provided for Windows 7, 64 bit, using the Microsoft Visual Studio 2010 compiler. Desmond using MPI is not supported under Windows. Format conventions Command lines appear in a typewriter font; in some cases, bolding draws your atten- tion 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 = { ... } } i ii 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 dis- cussed 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 outer- most to innermost, separated by 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. 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. • A boldfaced lowercase letter, such as a, is a vector of unspecified dimension, with th ai indicating the i element of the vector. • A boldfaced uppercase letter is a matrix of unspecified dimensions, though usually 3 × 3, 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 th 3n components, but instead ~ri denotes the i three-dimensional vector in r, which is the position of the ith particle in this case. Contents 1 Key Concepts 1 1.1 What is Desmond? . 1 1.1.1 Forces . 2 1.1.2 Particles . 3 1.1.3 Force fields . 4 1.1.4 Space . 4 1.1.5 Time . 5 1.1.6 Dynamics . 5 1.2 Using Desmond . 7 1.2.1 Input . 7 1.2.2 Applications and scripts . 7 1.2.3 Output . 8 1.2.4 Workflow . 8 1.2.5 Customizing Desmond . 10 2 Running Desmond 11 2.1 About configuration . 11 2.2 Invoking Desmond . 12 2.2.1 Using plugins . 14 2.3 Running Desmond in parallel . 16 2.4 Configuring Desmond applications . 17 2.4.1 mdsim . 17 2.4.2 remd . 19 2.4.3 minimize . 21 2.4.4 vrun . 22 2.5 Naming output files . 23 2.6 Configuring the built-in plugins . 24 2.6.1 anneal . 24 2.6.2 Biasing Force . 25 2.6.3 e bias .................................. 29 2.6.4 energy groups . 30 2.6.5 compute forces . 31 2.6.6 eneseq . 32 iii CONTENTS iv 2.6.7 maeff output . 33 2.6.8 posre schedule . 34 2.6.9 pprofile . 34 2.6.10 randomize velocities . 37 2.6.11 remove com motion . 37 2.6.12 trajectory . 38 2.6.13 status . 40 2.7 Configuring optional sections . 40 2.7.1 profile . 40 3 The Global Cell 43 3.1 Parallelization . 43 3.2 Configuration . 45 3.3 Migration . 47 4 Preparing a structure file 49 4.1 Converting a Desmond 2.0/2.2 structure file . 50 4.2 Preparing a Desmond DMS file . 50 4.2.1 Constructing an input DMS file for Viparr . 50 4.2.2 Running Viparr . 51 4.2.3 Adding constraints . 52 4.2.4 Running the build constraints program . 52 5 Calculating Force and Energy 53 5.1 Configuring force fields . 53 5.1.1 Force terms . 55 5.2 Bonded, pair, and excluded interactions . 55 5.3 Van der Waals and electrostatic interactions . 61 5.3.1 Near interactions . 64 5.3.2 Nonbonded tail corrections . 66 5.4 Nonbonded far interactions . 67 5.4.1 Electrostatic self-energy correction . 69 5.4.2 Virtual sites . 70 6 Constraints 73 6.1 Single precision resolution and constraints . 75 7 Dynamics 77 7.1 Particles and mechanics . 77 7.1.1 Particles . 77 7.1.2 Chemical systems . 78 7.2 Integrator . 78 7.3 RESPA . 79 7.4 Pressure . 80 v CONTENTS 7.5 Temperature . 81 7.6 Dynamical systems . 82 7.6.1 V NVE: Verlet constant volume and energy . 82 7.6.2 NH NVT: Nos´e-Hoover constant volume and temperature . 83 7.6.3 L NVT: Langevin constant volume and temperature . 84 7.6.4 Piston NPH: constant pressure and enthalpy . 86 7.6.5 MTK NPT: Martyna-Tobias-Klein, constant pressure and temper- ature . 89 7.6.6 L NPT: Langevin constant pressure and temperature . 90 7.6.7 Ber NVT: Berendsen constant volume and temperature . 92 7.6.8 Ber NPT: Berendsen constant temperature and pressure . 93 7.6.9 Brownian motion integrators . 95 7.6.10 The Multigrator integrator . 96 8 Free Energy Simulations 101 8.1 Configuring free energy simulations . 101 9 Enhanced Sampling and Umbrella Sampling 109 9.1 Introduction . 109 9.1.1 Who should read this chapter? . 109 9.1.2 Enhanced sampling functionality . 109 9.2 Using the Enhanced Sampling Plugin . 110 9.2.1 Workflow . 110 9.2.2 Output format . 110 9.2.3 Example configuration . 110 9.3 Interpreter . 111 9.3.1 Syntax . 111 9.3.2 Interpreter values . 112 9.3.3 Static Variables . 113 9.3.4 Function classes . 114 9.3.5 Functions . ..
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