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InfiniBand Cluster

Kreia is an Intel x86_64 cluster with 90 nodes. Each node has 8 processors and 12 GB of RAM memory. As a storage, kreia has a 4 Terabytes fibre channel Raid. Each node are interconnected using a technology known as Infiniband. InfiniBand is a switched fabric communications link used in high-performance computing and enterprise data centers. Its features include high throughput, low latency, quality of service and failover, and it is designed to be scalable. The InfiniBand architecture specification defines a connection between processor nodes and high performance I/O nodes such as storage devices.
This technology is specially design to improve the connection between nodes, so the parallelitation software such as MPI or MPICH play a very important role in the computing environment.


Each node has a solid state disk to increase, even more access for data. Computer simulations of the biomolecular processes in human cells guide better understanding of health and disease as well as development of dietary supplements and pharmacological treatments. Such simulations are extremely demanding and, in fact, all too often still limited by technological feasibility. However, technological advances are being brought to bear on computer simulations in biomedicine through highly dedicated biomedical engineers, who have often speerheaded uses of new computer technologies such that they became available in biomedicine much sooner than in other fields. A case in point is solid state disk (SSD) technology that can serve as extremely fast and large computer memory. Conventional RAM (random access memory) is fast, but limited in size due to cost; the well known hard disks (HDs) can hold large data sets at an affordable price, but are slow. The new SSDs are in the middle ground, faster than HDs, slower than RAM, offering large data storage at an affordable price. Modern uses of SSDs in smart phones and tablets attest to the usefulness of SSDs.

The InfiniBand architecture specification gives to kreia the possibility of running high computational jobs is a short time, so we mainly used this cluster for mollecular modelling a docking projects.

Some installed softwares are :

Gromacs
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the   Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily   designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated   bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions   (that usually dominate simulations) many groups are also using it for research on non-biological   systems, e.g. polymers.


Hex : Hex is an interactive protein docking and molecular superposition program. Hex understands protein and DNA structures in PDB format, and it can also read small-molecule SDF files. 

Plumed
PLUMED is an open source plugin for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular  focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.

NAMD : NAMD 
is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Charm
 (Chemistry at HARvard Macromolecular Mechanics):

  • is a versatile and widely used molecular simulation program with broad application to many-particle systems

  • has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments

  • provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques, and model-building capabilities

  • is useful for a much broader class of many-particle systems

  • can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models

  • has been ported to numerous platforms in both serial and parallel architectures