Adun

Deactivate terms in Forcefield for simulation

cavila — Mon, 14 Nov 2011 13:29:06 +0000

On some rare occasions you might wonder how a certain energy term shapes the energy landscape of your molecule.

Adun let’s you play with the forcefield turning on and off each of the energy terms during a simulation through the use of AdunShell.

Let’s see how to do it

First you create the template for your simulation (described elsewhere) setting the system, forcefields, simulator, etc.

In the command line you run

AdunShell -Template template.temp

which will start AdunCore and drop you into an interactive session inside the simulator. The interactive session begins after everything is set up and a number of the main objects (Configuration generator, force-fields etc) are already available. You will see a lot of log messages and then a greeting from AdunShell

Initially available objects:
Environment – The shell environment.
Simulator – The configuration generation object.
Systems – The collection of systems being simulated.
ForceFields – The collection of force-fields operating on the systems.
CheckpointManager – Object controlling the automatic collection of data.
Transcript – Object for displaying detailed strings (like a ‘print’ command’)To print a list of an objects methods use ‘methodNames’ e.g. ForceFields methodNames

Welcome to the Adun shell.

From here you can do whatever you want and then call production: to start the simulation as normal.

Plugin Installation Guide

mjohnston — Sat, 02 Apr 2011 14:29:08 +0000

We’ve updated the plugin installation guide (see here) plus new automatic installation packages for mac are available from download.gna.org/adun/MacPlugins.

Extending Force Fields

mjohnston — Thu, 24 Feb 2011 11:34:24 +0000

A common, and time-consuming, task in molecular simulation is creating entries for new molecules for a given force-field. The antechamber program from the Amber suite of tools handles most of the details of this process for Amber related force-fields. However to use it with Adun its output still needs to be converted to the FFML format. We’ve added a page describing exactly how to do this here.

The next step is adding the new molecule definitions to the force-field. A problem that often raises it head is conflicts between a force-field topology file containing custom molecules and general updates for the force-field. The current cvs version of Adun now separates custom extensions from the main topology file making it much easier to add molecules – see this page for more information.

Fedora & Suse Packages

mjohnston — Tue, 08 Feb 2011 10:52:16 +0000

RPMs for Adun are now available for Fedora and Suse. They are provided via dedicated repositories which allow Adun, and its dependencies, to be installed with a single command/click, and you can choose between “release” and “snapshot” package types.

See this page for more.

API Documentation

mjohnston — Wed, 02 Feb 2011 11:24:57 +0000

Extensive developer documentation (nearing 30,000 lines at the last count) for all Adun’s frameworks/libraries is now available online at http://home.gna.org/adun. This allows anyone interested to browse it and saves developers the hassle of keeping it up-to-date themselves.

However if your using a Mac its worth building the documentation locally as this allows you to browse it in Xcode in the same way as the Cocoa docs. See the INSTALL.Documentation file in the top level Adun source directory for more info.

Mac Source Install Guide

mjohnston — Wed, 26 Jan 2011 12:42:42 +0000

We’ve added a guide to installing Adun from source on a Mac. Its split into three steps:

A source Mac install is mainly for developers. If your unsure if this what you want we recommend you check the main install page. This describes the current installation options, the platforms they are available for, and what type of user they are most suited for, so you can choose the best installation method for your needs.

Linux Source Install Guide

mjohnston — Sun, 16 Jan 2011 16:17:45 +0000

We have extensively updated our guide to installing Adun from source on a Linux distribution. Its now split into three steps:

However first we recommend you check the main install page. This describes the current installation options, the platforms they are available for, and what type of user they are most suited for, so you can choose the best installation method for your needs.

Poster on Adun awarded in the VPH2010

jvilla — Mon, 03 Jan 2011 09:56:38 +0000

The poster entitled “Implementation of a multiscale model for molecular dynamics simulations of protein folding and aggregation in Adun” was awarded as the best one in the recent VPH2010 meeting in Brussels, as part of the VPH NoE dissemination activities. Nils Drechsel presented the poster in the conference.

Linking

mjohnston — Tue, 09 Nov 2010 16:14:44 +0000

The user manual has been extend with an entry describing linking – this is the ability to initialise the state (i.e. coordinates/velocities) of molecules in a simulation with their state from a checkpoint in another simulation. For example if you were a simulating a protein you could initialise it with a configuration generated from a previous minimisation run.

See here for more.

Threading

mjohnston — Mon, 01 Nov 2010 14:34:09 +0000

The current CVS of Adun now automatically threads nonbonded and Generalized Born calculations to multiple cores if they are available.

The attached graph shows the speed-up for Gas phase and GB simulations of a 6500 atom protein. Since the threading only applies to certain calculations you don’t get a linearly scaling speed-up. Instead the expected speed increase depends on the percentage time spent in the threaded calculations in serial – so bigger systems will show better scaling.

For this test case threading gives around a 4-5 times speed increase on six cores e.g. from 0.48 to 0.1 secs per step for 14 angstrom cutoff gas-phase (x4.8) and from 2.78 to 0.66 (x4.2) for 14 angstrom GB. The reason the GB calcs show less improvement with 4+ cpus seems to be related to memory access issues and we’re currently looking at how this can be improved.