title: QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.
abstract: The proper functioning of biomolecules in living cells requires them to assume particular structures and to undergo conformational changes. Both biomolecular structure and motion can be studied using a wide variety of techniques, but none offers the level of detail as do molecular dynamics (MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. Performing both simple and advanced MD simulations interactively, QwikMD automates as many steps as necessary for preparing, carrying out, and analyzing simulations while checking for common errors and enabling reproducibility. QwikMD meets also the needs of experts in the field, increasing the efficiency and quality of their work by carrying out tedious or repetitive tasks while enabling easy control of every step. Whether carrying out simulations within the live view mode on a small laptop or performing complex and large simulations on supercomputers or Cloud computers, QwikMD uses the same steps and user interface. QwikMD is freely available by download on group and personal computers. It is also available on the cloud at Amazon Web Services.
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.|Energy Biosciences Institute, University of Illinois at Urbana-Champaign, USA.
authors.forename: João V
authors.initials: JV
authors.lastname: Ribeiro
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.|Energy Biosciences Institute, University of Illinois at Urbana-Champaign, USA.
authors.forename: Rafael C
authors.initials: RC
authors.lastname: Bernardi
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.
authors.forename: Till
authors.initials: T
authors.lastname: Rudack
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.
authors.forename: John E
authors.initials: JE
authors.lastname: Stone
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Phillips
authors.affiliation: Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, USA.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Freddolino
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA.|Energy Biosciences Institute, University of Illinois at Urbana-Champaign, USA.|Department of Physics, University of Illinois at Urbana-Champaign, USA.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten