In addition to the GMX manual that we often see, there is a lot of information on the official website, more to see the benefits of understanding GMX, the following I put the official information on the Internet broadly listed, we look at the topic of interest:
Gromacs Total is divided into the following columns about Gromacsdeveloper Zone//If you want to change the source, to read this part documentation//GMX have a deep understanding downloads GPU acceleration// Starting with the 4.6 release, with the new GPU architecture, there are test parameters Gromacs papers//Initial literature jobs//recruitment project ideas//Proposed future projects support//HELP, which has information on training courses held, more practical, by thematic category documentation
- Acceleration and parallelization
- Cut-off schemes
- Errors
- FAQs
- Floating point Arithmetic
- How-Tos
- Adding a residue to a force Field
- Analysing trajectory information
- Beginners
- Carbon nanotube
- Changing a 3 point water model to a 4 point water model
- Checkpointing Jobs
- Constant PH Simulation
- Diffusion Constant
- Dihedral PCA
- Dihedral Restraints
- Distance Restraints
- Doing Restarts
- Essential Dynamics
- Extending simulations
- Free energy Calculations
- Plotting Data
- Build a Linux Cluster
- Making disulfide Bonds
- Membrane simulations
- Micelle Clustering
- Mixed Solvents
- Multiple Chains
- Multiple topology Entries
- Non-water solvation
- Normal Mode Analysis
- Parameterization of novel molecules
- PKa calculations
- Polymers
- Position Restraints
- Potential of Mean force
- Qmmm
- Reading XTC from Fortran
- Reducing trajectory Storage Volume
- REMD
- Removing fastest degrees of freedom
- Single-point Energy
- Speeding up simulations
- Steps to Perform a Simulation
- tabulated potentials
- Water solvation
- Tool Changes for 5.0
- Trajectory visualization
- Using Commands in Scripts
- Using VMD plugins to read trajectory formats not native to GROMACS
- Include File mechanism
- Installation Instructions 4.5
- Bluegene
- Cmake
- Compiling qmmm
- Cygwin
- Gromacs-openmm
- Intel (R) Cluster ready Reference
- Quick and Dirty Installation
- Windows
- Installation Instructions 4.6
- Installation Instructions 5.0
- Manual
- Performance checklist
- Terminology
- Average Structure
- Blowing up
- Energy Conservation
- Constraints and Restraints
- Molecular Dynamics Simulations
- Periodic boundary Conditions
- Pressure
- Reproducibility
- Thermostats
- Tutorials
- another lysozyme Tutorial
- free energy of solvation Tutorial
- GROMACS USA Workshop and Confere NCE
- An introduction-free Calculations:michael shirts, Session 2 a
- an introduction To replica Exchange Simulations:mark Abraham, Session 1 b
- Computing potentials of Mean Force:justin Lemkul, Session 2 A
- free energy calculation capabilities in Gromacs:michael shirts, session 1 B
- how long does I need to run my simulations? A Guide to thinking about convergence and Sampling:peter Kasson, Session 1 b
- large-scale automated ensemble si Mulation with GROMACS & Copernicus:iman Pouya, session 2 b
- membrane Simulations:justin Lemkul, session 1A
- parallelization schemes and GPU Acceleration:szilard Pall, Session 2 b
- topology preparation, "Wha T ' s in a log file ", basic performance Improvements:mark Abraham, Session 1 a
Gromacs Advanced Learning
