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Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, and their applications continue to be limited. They are limited in the number of atoms (often less than 100000), in time (rarely longer than few microseconds), and are severely restricted by the cost of computing resources.

In the last 20 years, we have observed amazing achievements, that are largely the result of use of expensive high-performance computer systems, like supercomputers, clusters and dedicated grids.

With the increase of system complexity, there is also an increase in usability complexity. The high cost of computational equipment and the difficulty in dealing with code for parallel or distributed computing, implies that the investigation of a biological system for more than a microsecond, is precluded to the large majority of life scientists.

We have created a system for distributed molecular dynamics (GRIMD) that is very easy to install and to run even for non-skilled scientists. GRIMD permits to exploit pc resources that in any department remains idle to run a large variety of calculations: from molecular dynamics to flexible docking, virtual screening and steered molecular dynamics.

The main advantages of GRIMD are:

    * Easy to install and to use even for not skilled users
    * Performances scale almost linearly up to thousand machines
    * Scripts of NAMD or YASARA can be distributed upon addition of few lines of code

 

 

GRIMD permits to distribute jobs of NAMD, YASARA*, AUTODOCK, MOPAC, Abalone and VINA on hundreds or thousands of computers with a very limited effort.

Autodock Vina Yasara
Mopac Namd
Abalone  

* Yasara is a licensed program. If you want to use GRIMD to run Yasara, you need to provide your license