Software

Initially, this will just be a list of some different softwares with links and short descriptions. If this turns out to be something useful I’ll try to structure this into subcategories for easy navigation. All the software listed here will be free, either as freeware, under academic license or in other ways or forms available without charge.

 

UCSF Chimera
This should maybe fall under the category of visualisation and analysis. Chimera is a program with a graphic user interface that can be used to visualise and analyse molecular structures and other related data (the list of things you can process and do is long) and kan handle molecular structure files, molecular dynamics simulation output, docking results and a whole lot more. I often use this software  when producing graphical material since it is exceptionally good at producing high quality pictures as well as animations.

There is plenty of well written tutorials for those who wants to learn “interactively” as well as a thorough and well written  manual. This makes it relatively easy to get started using the program. On top of this there is a fantastic “discussion forum” (mailing list) where helpful developers and users provide support, advice and help regularly.

What is truly remarkable is that this piece of software is made available free of charge, not only for academic use but also for personal use (for licensing details, visit the developer webpage). Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), supported in part by the National Institutes of Health (NIGMS P41-GM103311).

Apparently there is also something called ChimeraX available, I have not yet tested this piece of software myself and will have to return with information regarding functionality at a later time, as well as updating this section with some images and animations, possibly self produced material.

 

AMBER
Amber is a collection of softwares in a nice package for performing molecular dynamic simulations. The package itself is available in two different versions, AmberTools18 and Amber18. The reason why this is important is that AmberTools18 is available free of charge while Amber18 requires a license. AmberTools18 is completely independent of the software requiring a license while Amber18 requires a working installation of AmberTools18 to run.

The Amber webpage recommends the following articles providing a nice overview of the code.

  • R. Salomon-Ferrer, D.A. Case, R.C. Walker. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci. 3, 198-210 (2013). (PDF)
  • D.A. Case, T.E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005).

Without going into details, AmberTools18 is free, can be installed on a single computer with a single processor and capable of performing actual simulations and analysis of produced simulations. If a parallell compiled version of Amber (in particular the simulation engines including sander and premed for MPI execution) on a cluster, server or similar, a license is required. A license is not terrible expensive if you are using it for academic research, non-profit activities or government use (500 USD).

The Amber package is a fantastic resource for starting to learn simulation techniques and analysis much thanks to the available tutorials and manuals. There is also a very active mailing list where one can receive help and support from experienced users as well as developers. Many of the tutorials are updated for the current version of the software, unlike some of the other free software packages where tutorials are written for now outdated versions and not very easily adapted for someone without experience.

I could of course be a biased since this is the software which I am foremost using.

 

VMD (Visual Molecular Dynamics)

VMD is a program for simulating and displaying, animating and analysing molecules, simulations and more. The program supports most operating systems including OS X, Unix/Linux and Windows, the source code is freely available and VMD is available free of charge for academic and non-profit purposes, check the website for details regarding licenses.

VMD supports over 60 different types of file formats, a range of plugins are also available for analysis and manipulation of files and data, where the user can also write and share their own.

Both manual and tutorials are available for the software to get you up and started pretty fast. VMD is maintained by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign which are also supplying NAMD which is another molecular dynamics simulations and analysis package. Of course this software (NAMD) works very well together with VMD, it is also free and will be presented later on.

A personal reflection, I foremost use VMD to evaluate or modify simulations or structures. It is relatively easy on resources, loads quick and processes input files relatively fast as well. The user interface is not a appealing as the Chimera interface on the Mac however this is one reason for the low resource demand. Personally I have found VMD to be somewhat easier to use for analysis and evaluation of simulations an is somewhat quicker and has a somewhat broader range of possibilities through a built in Tk/Tcl command line however it does not reach quite the same standard as Chimera when producing high quality illustrations. This, however, might also depend heavily in experience and the somewhat more approachable meny system in Chimera that might have had a beneficial influence on my use and my opinion.

Read more about licensing and download the software on the VMD webpage and don’t forget to give cred where cred is due (cite).