AMBER

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	== Recommendations for Configuration and Usage ==		== Recommendations for Configuration and Usage ==
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-	Please describe here any common settings, configurations or conventions that would make the usage of this resource (library or tool) more interoperable or scalable across the HP-SEE resources. These recommendations should include anything that is related to the resource and is agreed upon by administrators and users, or across sites and applications. These recommendations should emerge from questions or discussions opened by site administrators or application developers, at any stage, including installation, development, usage, or adaptation for another HPC centre.
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-	Provided descriptions should describe general or site specific aspects of resource installation, configuration and usage, or describe the guidelines or convention for deploying or using the resource within the local (user/site) or temporary environment (job). Examples are:
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-	* Common configuration settings of execution environment
-	* Filesystem path or local access string
-	* Environment variables to be set or used by applications
-	* Options (e.g. additional modules) that are needed or required by applications and should be present
-	* Minimum quantitative values (e.g. quotas) offered by the site
-	* Location and format of some configuration or usage hint instructing applications on proper use of the resource or site specific policy
-	* Key installation or configuration settings that should be set to a common value, or locally tweaked by local site admins
-	* Conventions for application or job bound installation and usage of the resource

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Latest revision as of 08:04, 5 September 2011

Contents 1 Authors/Maintainers 2 Summary 3 Features 4 Architectural/Functional Overview 5 Usage Overview 6 Dependacies 7 HP-SEE Applications 8 Resource Centers 9 Usage by Other Projects and Communities 10 Recommendations for Configuration and Usage

• Web site: http://ambermd.org
• Described version: xx.xx
• Licensing: AMBER 11 software license agreements
• User documentation: link
• Download: link
• Source code: link

Authors/Maintainers

• Also origin, if the software comes from a specific project.

Summary

Assisted Model Building with Energy Refinement (AMBER) is a molecular dynamics software package that simulates a family of force fields for molecular dynamics of biomolecules. To use the AMBER force field, it is necessary to have values for the parameters of the force field (e.g. force constants, equilibrium bond lengths and angles, charges). A fairly large number of these parameter sets exist. It is written in Fortran and C with support for most major Unix-like systems and compilers. Development is conducted by a loose association of mostly academic labs. The package is divided into two parts: AmberTools, a collection of freely available programs mostly under the GPL license, and Amber11, which is centered around two main simulation programs, and which is licensed under a more restrictive license. These two programs are as follows:

• SANDER (Simulated Annealing with NMR-Derived Energy Restraints) – the central simulation program and provides facilities for energy minimization and molecular dynamics with a wide variety of options
• pmemd – a feature-limited reimplementation of SANDER, designed with parallel processing in mind.

It is well known that SANDER is not as good in terms of scalability as pmemd. Fortunately in one of the main applications that use AMBER we concluded that pmemd may be used for most of the simulations.

Features

• Listed features

Architectural/Functional Overview

• high level design info, how it works, performance - may be a link, or several links

Usage Overview

• If possible with small example - may be a link

Dependacies

• list of all relevant dependencies on other libraries

HP-SEE Applications

• PCACEC (Principal Component Analysis of the Conformational Interconversions in large-ring Cyclodextrins)
• FMD-PA (Design of fullerene and metal-diothiolene-based materials for photonics applications)

Resource Centers

• RCs supporting it (with version number if not the same as above)

Usage by Other Projects and Communities

• If any

Recommendations for Configuration and Usage