ParmBSC1 forcefield Nucleotide MD Simulations Database
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ParmBSC1 Portfolio, a BigData approach to efficiently manage large nucleic acids simulation data.
Software
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 |