About UAMMD-structured

What is UAMMD-structured and what is not?
UAMMD-structured compilation and installation
First Example

UAMMD-structured Guide

Simulation
Execution
Input
System
- Handling Errors
Global
- Fundamental
- Units
- Types
- Ensemble
State
Integrators
Topology
- Structure
- Force Field
Simulation Steps

Global Data

Fundamental
Units
- None
- KcalMol_A
Types
- Basic
- Polarizable
Ensemble
- NVT
- NVTlambda

Integrators

Minimization
- SteepestDescent
NVE
- Verlet
  - VelocityVerlet
NVT
Special
- None

Interactors

Bonds
Single
- External
- Surface
NonBonded
- Short Range
- Electrostatics
Set
- Set1
- Set2
Atomic Force Microscopy
- SphericalTip
- SphericallyBluntedConicTip

Data Structures

VerletConditionalListSet
- Condition

Simulation Steps

SimulationUtils
- UtilsStep
  - InfoStep
  - SortStep
- FlowControl
SimulationOutput
- WriteStep
  - WriteStep
  - WritePatchyParticlesStep
SimulationMeasures

Utilities

Groups
Scheduling the components
Batching

pyUAMMD

Introduction
Installation
- Installing from conda (recommended)
- Installing from source
  - Building UAMMD-structured and pyUAMMD
  - Building pyUAMMD when UAMMD-structured is already installed

Implementation

Input
Design
- Simulation
- System
- Global
- State
- Integrators
- Topology
  - Structure
  - Force Field
Extending UAMMD-structured
Information for developers
- Github actions

Online Examples

Online Examples

UAMMD-structured

Bonds
Bond2
HelixExponential
View page source

HelixExponential

Note

Work in progress.

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© Copyright 2023, Pablo Ibáñez-Freire.

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