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Volume 7


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In Silico Biology 7, 0008 (2006); ©2006, Bioinformation Systems e.V.  



GUIMACS - A Java based front end for GROMACS

Pradeep Kota

Centre for Biotechnology, Anna University, Chennai, INDIA


* Corresponding author
  Email: kotaonline@gmail.com


Edited by E. Wingender; received September 07, 2006; revised November 17, 2006; accepted November 26, 2006; published January 05, 2007


Abstract

Molecular dynamics simulations have gained importance due to their ability to provide valuable insights into understanding structure-function relationships of biological macromolecules. With increasing computational speeds there has been a substantial demand for optimization of simulation algorithms to obtain results even faster. With this on one hand, the need for ease of operation lies on the other. GUI front end programs are important appurtenances to ease the use of command line programs. Effective use of command line based programs requires basic knowledge of the UNIX shell and at least one of the UNIX based text editors, making it difficult for pure biologists to use them efficiently. GROMACS, a widely used suite of molecular dynamics simulation and analysis programs, is no exception to this. As a matter of fact, the increasing dependency of experimental procedures on computational methods for accentuating certain key experimental findings increases the need for interactivity in use of command-line based packages.

GUIMACS is a Java based user-interactive front-end interface for the Linux version of GROMACS (version 3.3). GUIMACS runs as a standalone application with Multiple Document Interface (MDI) enabling its users to run and/or analyze multiple molecular dynamics simulations simultaneously.


Keywords: GROMACS, GUI front-end, Java interface, molecular dynamics