Joao V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C.
Phillips, Peter L. Freddolino, and Klaus Schulten.
QwikMD-integrative molecular dynamics toolkit for novices and
experts.
Scientific Reports, 6:26536, 2016.
(PMC: PMC4877583)
RIBE2016
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.
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