Software¶
Summary¶
NBD main technologies are:
PELE++ (PELE docs)
PELE Platform (PELE Platform)
Adaptive PELE Simulation (Adaptive PELE docs)
Frag PELE Simulation (FrAG PELE docs)
MSM PELE Simulation (MSM PELE docs)
NAMD Molecular Dynamics (NAMD docs)
analogs finder (analogs finder docs)
modtox AI (modtox AI docs)
schrodinger platform (schrodinger docs)
GROMACS (GROMACS docs)
PLUMED (PLUMED docs)
Job Launching Templates¶
PELE¶
Pele is our in-house commercial software that we sell and use for speeding up DD projects
NAMD¶
NAMD is used to perform molecular dynamics over several systems to study their dynamics over time
Schrodinger¶
Schrodinger is used for virtual screening purposes and system preparation.
Python packages¶
A miscelaneous of several Python Packages built along the years
GROMACS¶
GROMACS is a versatile package to perform molecular dynamics.
PLUMED¶
PLUMED is a plugin that works with a large number of molecular dynamics codes. PLUMED can also work as a Command Line Tool to perform analysis on trajectories saved in most of the existing formats.
PSI4¶
PSI4 is the latest in the family of PSI Quantum Chemistry programs, it’s mainly developed at Dave Scherrill’s lab. at Georgia Tech. It’s focused on the highest levels of Quantum Chemistry calculations such as fullCI, Coupled Cluster Theory and various DFT recipes.
Nice DCV¶
NICE DCV is the remote 3D visualization technology that enables Technical Computing users to connect to OpenGL applications running in a data center. (https://aws.amazon.com/es/hpc/dcv/)
Tests¶
Here you will find information of the automatic tests run on nbdcalc01 computer
New Comers¶
Here you will find how to set up your laptop to access NBD facilities
AlphaFold¶
Here you will find how to run AlphaFold
Structure Filtering¶
Here you will find how to run a structure filtering
Protein-protein docking¶
Here you will find information about several PPI software installed in our cluster