An Overview of Information Flow in AMBER
Overview
Teaching: 30 min
Exercises: 5 minQuestions
What files are needed to run an MD simulation with AMBER?
Objectives
Learn what types of files are needed to run an MD simulation with AMBER
Introduction
Information flow in AMBER
Simulation workflow in MD usually involves three steps: system preparation, simulation, and analysis. Let’s take a closer look at these steps.
flowchart TB
style Q stroke-dasharray: 5 5
style T stroke-dasharray: 5 5
subgraph "Prepare"
A(["PDB files"]) ==> |Load
coordinates| C{TLEAP,
XLEAP} B([FF files]) --> |Load
parameters|C H([LEaP commands])-->|Build
simulation system|C end subgraph "Run MD" C-->|Save
topology|D(["prmtop"]) C==>|Save
coordinates|E(["inpcrd"]) E==>|Load
coordinates|F Q([disang])-.->|Load
NMR restraints|F T([groupfile])-.->|Setup
multiple
simulations|F G(["mdin"])-->|Load
run options|F D-->|Load
topology|F{SANDER,
PMEMD} F==>|Save
restart|P([restrt]) P==>|Load
restart|F end subgraph Analyze N(["CPPTRAJ
commands"])-->|Run
analysis|J F===>|Save
trajectory|I([mdcrd, mdvel]) F--->|Print
energies|L([mdout,
mdinfo]) L-->|Load
energies|J I==>|Load
frames|J{CPPTRAJ,
PYTRAJ} I==>|Load
frames|K{MMPBSA} R([MM-PBSA
commands])-.->|Compute
PB energy|K J-->S[Results] K--->S((Results)) end D---->|Load
topology|J linkStyle 1,3,9,21 fill:none,stroke:blue,stroke-width:3px; linkStyle 2,8,12 fill:none,stroke:red,stroke-width:3px;
coordinates| C{TLEAP,
XLEAP} B([FF files]) --> |Load
parameters|C H([LEaP commands])-->|Build
simulation system|C end subgraph "Run MD" C-->|Save
topology|D(["prmtop"]) C==>|Save
coordinates|E(["inpcrd"]) E==>|Load
coordinates|F Q([disang])-.->|Load
NMR restraints|F T([groupfile])-.->|Setup
multiple
simulations|F G(["mdin"])-->|Load
run options|F D-->|Load
topology|F{SANDER,
PMEMD} F==>|Save
restart|P([restrt]) P==>|Load
restart|F end subgraph Analyze N(["CPPTRAJ
commands"])-->|Run
analysis|J F===>|Save
trajectory|I([mdcrd, mdvel]) F--->|Print
energies|L([mdout,
mdinfo]) L-->|Load
energies|J I==>|Load
frames|J{CPPTRAJ,
PYTRAJ} I==>|Load
frames|K{MMPBSA} R([MM-PBSA
commands])-.->|Compute
PB energy|K J-->S[Results] K--->S((Results)) end D---->|Load
topology|J linkStyle 1,3,9,21 fill:none,stroke:blue,stroke-width:3px; linkStyle 2,8,12 fill:none,stroke:red,stroke-width:3px;
System Preparation
- Two utilities for simulation preparation: tLEaP and xLEaP.
- The command line version (tLeap) is very efficient for executing scripts automatically.
- The GUI version (xLEaP) is good for building simulation systems interactively.
Simulation
- Two MD engines: SANDER and PMEMD.
- Parallel (MPI) SANDER
- Parallel and GPU-accelerated PMEMD
- PMEMD is faster than SANDER, but it has fewer options
Analysis
- CPPTRAJ (command-line pytraj)
- PYTRAJ (python front end to ptraj)
- MMPBSA
Other useful utilities:
- antechamber (topology builder)
- parmed (utility for topology editing and conversion)
- quick (GPU-accelerated DFT QM program)
- packmol-memgen (utility for preparing membrane systems)
Key Points
To run an MD simulation with AMBER 3 files are needed: an input file, a parameter file, and a file describing coordinates/velocities .