ParmBSC1 forcefield Nucleotide MD Simulations Database

ParmBSC1 Portfolio, a BigData approach to efficiently manage large nucleic acids simulation data.


ParmBSC1 portfolio is powered by an Apache 2. web server with PHP 5, Mongo 2.6.2 and Cassandra ?.?.

List of external software used in ParmBSC1 portfolio and NAFlex operations:

Program Description Package & Version
MongoDB BigData Document-oriented DB MongoDB v.2.6.2
Apache Cassandra BigData Column-oriented DB. Cassandra ?.?
Curves+, Canal Analysis of Nucleic Acids Structure and Flexibility Curves+ 2.0
R Statistics Statistical Computing and Graphics software. R 2.15.0
Gnuplot Plotting tool Gnuplot 4.2
Grace Plotting tool Grace 5.1.21
GROMACS tools Molecular Dynamics Package Tools GROMACS 5.0
JSMol Molecular Graphics Viewer JSMol 14.0.5
PCAsuite Trajectory compression tool PCASuite 1.1
Ptraj, cpptraj Structure and dynamic analysis of trajectories Ambertools 14
tgatoppm, pnmcrop, pnmtopng Image management Netpbm 10.0
VMD Molecular Graphics Viewer VMD 1.8.5
ffmpeg Video management ffmpeg 2.5
MDAnalysis Python toolkit to analyze MD trajectories MDAnalysis