NAMD 2.14 User's Guide
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NAMD User's Guide
Version 2.14
R. Bernardi, M. Bhandarkar, A. Bhatele, E. Bohm, R. Brunner, R. Buch, F. Buelens, H. Chen, C. Chipot, A. Dalke, S. Dixit, G. Fiorin, P. Freddolino, H. Fu, P. Grayson, J. Gullingsrud, A. Gursoy, D. Hardy, C. Harrison, J. Hénin, W. Humphrey, D. Hurwitz, A. Hynninen, N. Jain, W. Jiang, N. Krawetz, S. Kumar, D. Kunzman, J. Lai, C. Lee, J. Maia, R. McGreevy, C. Mei, M. Melo, M. Nelson, J. Phillips, B. Radak, J. Ribeiro, T. Rudack, O. Sarood, A. Shinozaki, D. Tanner, P. Wang, D. Wells, G. Zheng, F. Zhu
August 5, 2020
Theoretical Biophysics Group
University of Illinois and Beckman Institute
405 N. Mathews
Urbana, IL 61801
Description
The NAMD
User's Guide
describes how to run and use the
various features of the molecular dynamics program NAMD.
This guide includes the capabilities of the program, how
to use these capabilities, the necessary input files and
formats, and how to run the program both on uniprocessor
machines and in parallel.
NAMD development is supported by National Institutes of Health
grant NIH P41-GM104601.
NAMD Version 2.14
Authors: R. Bernardi, M. Bhandarkar, A. Bhatele, E. Bohm, R. Brunner, R. Buch, F. Buelens, H. Chen, C. Chipot, A. Dalke, S. Dixit, G. Fiorin, P. Freddolino, H. Fu, P. Grayson, J. Gullingsrud, A. Gursoy, D. Hardy, C. Harrison, J. Hénin, W. Humphrey, D. Hurwitz, A. Hynninen, N. Jain, W. Jiang, N. Krawetz, S. Kumar, D. Kunzman, J. Lai, C. Lee, J. Maia, R. McGreevy, C. Mei, M. Melo, M. Nelson, J. Phillips, B. Radak, J. Ribeiro, T. Rudack, O. Sarood, A. Shinozaki, D. Tanner, P. Wang, D. Wells, G. Zheng, F. Zhu
Theoretical and Computational Biophysics Group, Beckman Institute, University of Illinois.
©1995-2018 The Board of Trustees of the University of Illinois.
All Rights Reserved
Contents
List of Figures
Introduction
Getting Started
Input and Output Files
NAMD configuration parameters
AMBER file and force field support
GROMACS file support
Creating PSF Structure Files
BPTI Example
Using generated files in NAMD.
Building solvent around a protein
New Commands in the version 2.0
List of Commands
Example of a Session Log
Force Field Parameters
Non-bonded interactions
Water Models
Drude polarizable force field
MARTINI Residue-Based Coarse-Grain Forcefield
Constraints and Restraints
Generalized Born Implicit Solvent
3-Phase Calculation
Configuration Parameters
Standard Minimization and Dynamics Parameters
Energy Minimization
Dynamics
Temperature Control and Equilibration
Pressure Control
User Defined Forces
Interactive Molecular Dynamics (IMD)
Tcl Forces and Analysis
Tcl Boundary Forces
External Program Forces
Collective Variable-based Calculations (Colvars)
Configuration syntax used by the Colvars module
Global keywords
Input state file
Output files
Defining collective variables
Angles
Contacts
Collective metrics
Rotations
Protein structure descriptors
Raw data: building blocks for custom functions
Geometric path collective variables
Arithmetic path collective variables
Volumetric map-based variables
Shared keywords for all components
Periodic components
Non-scalar components
Linear and polynomial combinations of components
Custom functions
Scripted functions
Defining grid parameters
Trajectory output
Extended Lagrangian
Multiple time-step variables
Backward-compatibility
Statistical analysis
Selecting atoms
Treatment of periodic boundary conditions.
Performance of a Colvars calculation based on group size.
Biasing and analysis methods
Extended-system Adaptive Biasing Force (eABF)
Metadynamics
Harmonic restraints
Computing the work of a changing restraint
Harmonic wall restraints
Linear restraints
Adaptive Linear Bias/Experiment Directed Simulation
Multidimensional histograms
Probability distribution-restraints
Defining scripted biases
Performance of scripted biases
Scripting interface (Tcl): list of commands
Syntax changes from older versions
Alchemical Free Energy Methods
1
Implementation of the free energy methods in NAMD
Examples of input files for running alchemical free energy calculations
Description of a free energy calculation output
Hybrid single-dual topology approach for relative binding
free energy calculation of ligand to receptor
Accelerated Sampling Methods
Gaussian Accelerated Molecular Dynamics
Solute Scaling and REST2
Adaptive Tempering
Locally enhanced sampling
Replica exchange simulations
Random acceleration molecular dynamics simulations
Structure based simulations
Running SMOG simulations
Constant-pH Simulations
1
Minimal Examples
Hybrid QM/MM Simulations
Custom Quantum Chemistry Software
Independent QM Regions
Keywords
Runtime Analysis
Performance Tuning
Non-bonded interaction distance-testing
Translation between NAMD and X-PLOR configuration parameters
Sample configuration files
Running NAMD
NAMD Availability and Installation
Bibliography
Index
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