Please note: The FAQ pages at the HPCVL website are continuously being revised. Some pages might pertain to an older configuration of the system. Please let us know if you encounter problems or inaccuracies, and we will correct the entries.

This is a "Frequently Asked Questions" file on using the molecular-dynamics program suite "Amber" on the SunFire 6800 cluster. These programs are suitable to carry out molecular dynamics simulations on large molecules, especially biomolecules.

What is "Amber"?

Amber is a suite of programs that allows the user to carry out molecular dynamics simulations. It is particularly well-suited for calculations on biomolecules. The suite consists of the following parts:

a. LEaP is a program to set up a new system or modify an existing one.

b. Antechamber is used to include standard nucleic acids or proteins.

c. Sander is the basic molecular dynamics / energy optimization program.

d. Gibbs is a free-energy perturbation program.

e. Nmode is used for vibrational analysis.

f. Anal is used for the structural analysis of a specific configuration of the system.

g. Ptraj analyses trajectories from a molecular dynamics run.

h. Carnal is an alternative molecular-dynamics analysis program (somewhat complementary to Ptraj).

i. Nmanal and Lmanal compute atomic fluctuations and correlation functions.

j. MM-Pbsa is a script file that performs an automatic analysis of molecular-dynamics "snapshots"

This list also gives a simple overview of the capabilities of Amber. The current version of Amber running on HPCVL machines is Amber 9. The most current version is version 11.

Where is "Amber " located and how do I access it?

Before you can access Amber, you need to read our license agreement and sign a statement that you have done so and will abide by it. See the last section for details.

The Amber program suite is located in the directory /opt/amber. To access it, you have to either include this directory in your path:

export PATH=$PATH':/opt/amber/exe'

Alternatively, you can use "usepackage" to set up Amber. In that case, you just need to type

use amber

and you're done. This command can also be put into your setup file (for intance, .bash_profile) to avoid having to type it every time you want to use Amber.

How do I run "Amber"?

This portion of the FAQ is still under construction. The usage of Amber is explained in detail in the Amber 9 User's Manual which is available for download in pdf format.

Can I run Amber in parallel?

Yes. Amber is inherently parallelized and designed to scale well on a multi-processor machine or a cluster. The underlying parallel system is MPI (Message Passing Interface) which is a commonly available standard that runs on many platforms. Consult our MPI FAQ and follow some of the links in there if you want to have more information about MPI. If you want to use multiple processors for your Amber run, you have to submit the program to a parallel environment. In the case of our main production machines, this environment is called ClusterTools, and the relevant command is mprun:

mprun -np 8 program_name < input_file >output_file

This will run your program on eight processors.

Note that you are only allowed to run Amber this way for small test systems! For any production jobs, you have to submit the task to the GridEngine queuing software (see next section).

How do I set up and run a Amber batch job?

This portion of the FAQ is still under construction. Production jobs are submitted on the SunFire systems via the GridEngine, which is a load-balancing software. To obtain details, read our GridEngine FAQ, especially the parts dealing with MPI jobs.

Where can I get further help?

AMBER is a complex software package, and requires practice to be used efficiently. In this FAQ we can not explain it use in any detail. Complete documentation for the program is available in the form of the User's Manual, which is an absolute must-have if you want to use this program. It is available at the official Amber website. This website is also your number-one address if you have questions about the program or encounter problems. They feature a very useful FAQ and even tutorials. Unfortunately, most of the webpage refers to the most recent Amber version.

If you are experiencing trouble running a batch command script or with the GridEngine, read our FAQ on that subject, and maybe consult the manual for that software which is accessible as a PDF file.

HPCVL also provide user support in the case of technical problems.Contact us here, we might be able to help, or pass you on to someone who can.

How is Amber licensed?

Amber is licensed software. The distributors of Amber require their users to sign a License Agreement, and HPCVL has done so. The License Agreement restricts usage of the Amber installation to academic research purposes, specifically excluding commercial or contract use. Like with other software, HPCVL requires users who want to use Amber, to read this agreement, and sign a statement that they have done so. The agreement can be downloaded here . Please also download the statement , sign it and return it to us. You will then be included in a Unix user group that has access to the Amber executables.