Desmond Tutorial

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Notice The Desmond Tutorial 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 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 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 © 2008 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. September 2008
Preface Intended Audience This tutorial is intended for computational chemists using Desmond in setting up and running 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 3 (RHEL3) or later. Linux clusters can be networked with either Ethernet or Infiniband ® . Viparr requires a recent version of Python; we recommend Version 2.5.1. This tutorial assumes that someone has prepared the Desmond‐Maestro environment for you, either by installing the packages available from Schrödinger LLC or the Academic release of Desmond available from D. E. Shaw Research. Where noted, the procedures described in the tutorial make use of software that is not included in the Academic version. In those cases the software is available from Schrödinger. September 2008 D. E. Shaw Research i
Page 1: Desmond Tutorial Desmond Version 2.
Page 5 and 6: from outermost to innermost, separa
Page 7 and 8: Contents Preface . . . . . . . . .
Page 9 and 10: Loading Files from the Command Line
Page 11 and 12: List of Figures Figure 1.1: Simulat
Page 13 and 14: 1 Desmond Tutorial Introducing Desm
Page 15 and 16: Desmond Tutorial Tutorial Steps Fig
Page 17 and 18: Desmond Tutorial Tutorial Steps 3.
Page 27 and 28: Desmond Tutorial Tutorial Steps Sys
Page 31 and 32: 2 Learning the Maestro- Desmond Env
Page 33 and 34: Learning the Maestro-Desmond Enviro
Page 41 and 42: 3 Preparing Proteins with Missing R
Page 43 and 44: Preparing Proteins with Missing Res
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Preparing Proteins with Missing Res
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4 Preparing a Desmond simulation wi
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Preparing a Desmond simulation with
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5 Finishing Preparations for Desmon
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Finishing Preparations for Desmond
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6 Running Desmond Simulations Overv
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Running Desmond Simulations Running
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7 Preparing Free Energy Perturbatio
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Preparing Free Energy Perturbation
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8 Visualization and Analysis using
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Visualization and Analysis using Ma
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9 Analyzing Trajectories Using VMD
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Analyzing Trajectories Using VMD Lo
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Analyzing Trajectories Using VMD Ge
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10 Documentation Resources Detailed
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