Desmond Tutorial

Desmond User’s Guide
About this Guide
Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 7
Chapter 8
Chapter 9
Chapter 10
This manual contains the following sections:
describes Desmond and outlines the steps to perform a simulation on a simple protein.
describes the Desmond‐Maestro environment, focusing on the tools and facilities available
in Maestro for manipulating molecular systems.
describes how to use Schrödinger’s Prime utility for repairing proteins with missing residues
or side chains.
describes the System Builder, the tool for setting up molecular systems for simulation
using Desmond
describes force field parameter assignment program Viparr and making changes to the
configuration file output by the system builder.
describes how to run Desmond within the Maestro environment and from the command
line.
describes Free Energy Perturbation simulation using Maestro workflow.
describes how to view the results of Desmond simulations in Maestro.
describes VMD, an alternate workflow available separately from the University of Illinois,
that can also be used to view trajectories and analyze the results of simulations.
provides pointers to additional documentation on Desmond‐Maestro system.
Format Conventions
Command lines appear in a monospaced font; in some cases, bolding draws your attention
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 = t 1
checkpt = { ... }
plugins = [ ... ]
... }
Configuration files are divided into sections, which can in some cases 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 parameters
appear as a keypath, in which the name of each enclosing section appears in order
ii D. E. Shaw Research September 2008