MDWeb is powered by an Apache 2. web server with PHP 5. and MySQL 5.0.51. Calculations are redirected to a 8 core Intel(R) Xeon(R) CPU @ 2.67GHz - 16GB RAM cluster managed by a Sun Grid Engine batch manager.

List of external software used in MDWeb operations:

Program Description Package & Version
Biomoby Biomoby web-services framework BioMoby 1.0
BLAST Basic Local Alignment Search Tool BLAST 2.2.17
CMIP Classical Molecular Interaction Potential CMIP 2.5.4
Gnuplot Plotting tool Gnuplot 4.2 patchlevel 2
Grace Plotting tool Grace 5.1.21
GROMACS Molecular Dynamics Simulator GROMACS 4.5.5
JSMol Molecular Graphics Viewer JMol 14.0.5 (HTML5)
MobyLite PerlAPI BioMoby Perl API MobyLite PerlAPI 1.0
NAMD Molecular Dynamics Simulator NAMD 2.8
PCAsuite Trajectory compression tool PCASuite 1.1
PropKa Prediction of protein pKa values Propka 2.0
Ptraj, cpptraj Structure and dynamic analysis of trajectories Ambertools 12
tgatoppm, pnmcrop, pnmtopng Image management Netpbm 10.0
Tleap MD preparation program Ambertools 1.2
VMD Molecular Graphics Viewer VMD 1.8.5
Curves+, Canal Analysis of Nucleic Acids Structure and Flexibility Curves+ 2.0
X3DNA Analysis, rebuilding and visualization of 3D-Nucleic Acid containing structures. X3DNA 2.0
Open Babel Chemical toolbox designed to speak the many languages of chemical data. Open Babel 2.1.1


NAMD BioMoby
AmberTools Gromacs
JMol Sun Grid Engine
FlexServ MoDEL