EaStCHEM RCF Homepage | Support Pages | Software Information
Amber
Amber is a set of tools and forcefields for performing classical simulations. It is particularly designed to be used on biological systems. More information can be found at the Amber website.
Documentation
The Amber 9 manual is available online.
Running
The Amber package consists of many different programs and utilities and each of them is run in a different way. As a rule of thumb, utility packages are run from the command line in an interactive manner whilst any computationally demanding packages are run through the queuing system. A list of how to submit different Amber jobs that require the queuing system is given below. Any programs that are not listed should be run interactively from the command line.
A sander (the simulation module of Amber) job is submitted to the cluster queuing system using the sandersub command. For example:
> sandersub -np 8 -q parallel-medium.q test
This would submit a sander job to the parallel-medium.q queue using 8 processors and the input in the files test.in, test.inpcrd and test.prmtop. sander can run in serial or distributed memory form.
For more information on sandersub see the EaStCHEM Submission System User Guide.