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Friday22 October 2021

How to effectively run molecular dynamics simulations with AMBER?

amberToday we are going to review a case study of University of Illinois “Accelerated molecular modelling enables rapid response to H1N1” that shows how scientists could efficiently run multiple simulations and potentially achieve life-saving results faster.

In response to a global pandemic, like Influenza A, requires a quick development of drugs to effectively treat a new virus that is likely to evolve. A research group of University of Illinois, Urbana- Champaign, was using Amber Molecular Dynamics, a suite of computational chemistry programs and force fields for molecular dynamics, on its study of Influenza A (H1N1) virus. The main challenge for the scientists was the duration of each simulation cycle per day as more simulations meant faster time to discovery.

Development of drugs comprises several processes, one of which is a compute-intensive process that is used to define how mutations of the flu virus protein could disrupt the binding pathway of the vaccine Tamiflu, rendering of this process could be potentially ineffective. This determination involved a daunting simulation of a 35,000- atom system, something that Urbana- Champaign scientists decided to tackle in a new way using NVIDIA GPUs. Managing these simulations on a CPU could take more than a month to calculate, and that would only amount to a single simulation, not the multiple simulations that constitute a complete study.


HPC As A Service

HPC As A Service
, discover its advantages today!

I would like to start off by citing the statement used in one of IDC’s industry reports that clearly highlights the importance of HPC sector in the modern society:

“Today, to Out-Compute is to Out-Compete”

I believe that this quote brings to our attention the fact that nowadays HPC is not only used by the government or large scientific groups but is well on its way to being an indispensable tool for SMEs and business of all kinds. Every day we see more and more professionals across numerous industries like Oil & Gas, Finance, Capital Markets enquiring about the potential advantages of HPC to their particular firm or enterprise.

And this is only the beginning, according to many recent reports the need for High Performance Computing will continue to grow. Analysts from Gartner, for example, expect worldwide IT spending to total of $3.7 trillion in 2013, which is 4.2 percent up on 2012 spending, however especial expansion has been predicted for Cloud Computing.

In the past few years we could see a number of small, medium as well as large companies suffering from the recession, as the outcome current economic conditions force them to maintain capital spending restrictions even in mission critical areas such as HPC.


Accelerating reservoir simulation with GPUs.

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Accelerating reservoir simulation with GPUs.

Get your results in hours vs days!

As large and complex computational problems become more and more common across numerous industry segments, the need of  computation by HPC (High Performance Computing) industry increases. However, traditional CPU technology is no longer capable of scaling in performance sufficiently to address this demand.

The parallel processing capability of the GPU allows it to divide complex computing tasks into thousands of smaller tasks that can be run concurrently. This enables computational scientists and researchers to address some of the world’s most challenging computational problems up to several times faster; and reservoir simulation could be one of those challenges.

What is the purpose of Reservoir Simulation?
Reservoir simulation models are used by oil and gas companies in the development of new fields. Also, models are used in developed fields where production forecasts are needed to help make right investment decisions. Reservoir Simulation has two main goals: Determine best locations and schedules for wells to optimize production and predict future production rate (from a reservoir model).


GPU & CPU Rendering

GPU & CPU rendering.
Less Time on Waiting & More Time for Creating.

Today I would like to talk about one of the biggest headaches of all the animators, as well as professionals of architectural and interior design studios- graphics rendering. First, allow me to start by defining the rendering process.

Nowadays computer graphics play significant role in our day-to-day life and we often see it in movies with spec effects, cartoons, TV & print advertisement; and this list goes on forever. All this stuff, that we like so much, is designed with the help of special programs that are specialized in creating models (Autodesk 3ds Max, Maya) and in applying all the effects that designer wants (rendering), as well as in providing us with the end image (V-Ray, Mental Ray).

So, what is rendering? Rendering is the process of generating an image from a model. And model is actually a scene file that contains detailed information about the model: its shape, coordinates, textures that cover it, effects like shading and lighting which are applied to the model, viewpoint from which we look at the model, and etc.


Before Rendering 


After Rendering 


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