Training (NEW)

ARCHIE-WeSt Training

ARCHIE-WeSt support Team offers Introductory Training for all ARCHIE-WeSt users as well as Advanced Training in Molecular Dynamics

Induction Training

Induction training is offered free of charge for all new ARCHIE-WeSt users based on demand, usually twice per month. Training is delivered by Dr Karina Kubiak – Ossowska (ARCHIE-WeSt User Support Officer,


1. Basic Linux Training

This 2-hour training session is dedicated for those ARCHIE-WeSt users that have never used Linux operating system before or are not very familiar with Linux. The training will cover:

* basic navigation under Linux: creation,  changing, copying, moving or deleting the file(s) or the directory(s); listing files and directories; file compression

* text editors

* file permissions

* remote control (login, data transfer)


2. Basic HPC Training

This 2-hour training g is dedicated for all new ARCHIE-WeSt users and will cover:

* basic specification of the system

* remote access

* job control (launching, deleting, monitoring the progress)

* code of conduct


Advanced Training

Advanced training is dedicated for ARCHIE-WeSt users that are familiar with using HPC systems.


1. Basic Principles in Molecular Dynamics Theory

It is suggested to participate also in VMD and NAMD training sessions. This training course will cover:

* basic principles of MD

* the force-field idea

* potential energy minimization procedures

* integration (solving) of  Newton’s equation of motion

* MD algorithm

* thermostat

* constraints and algorithms

* Steered Molecular Dynamics (SMD)


2. Molecular dynamics simulations in NAMD

It is suggested to participate also in VMD and basic principles in MD theory training sessions. This training will cover:

A. Running MD simulations in NAMD:

* from protein structure to MD simulations

* system neutralisation and solvation

* minimization, equilibration, heating

* the trajectory calculations

B.  Advanced MD simulations

* Steered MD (SMD)

* Particle Mesh Ewald (PME) method


3. Visualization in VMD

This training session is dedicated mainly for people running Molecular Dynamics simulations, nevertheless it is possible to use VMD for other purposes.  This training will cover:

* loading the file (molecule) and information file (psf file, trajectory file)

* display methods

* graphical representations, selections

* labelling, changing the font

* making a nice figure and movie

* using tcl scripts

* structure analysis

* modelling using VMD (adding ions, solvatation)