MD Darshan

MD Darshan: Your Molecular Design tool for Product Development & R&D

(Developed by Omkar Patil and Sanat Mohanty)
Molecular simulation and design tools have seen limited use by experimentalists and product
developers because:
1. They are too slow with respect to the needs of product developers. Typical times of 3-10 days for each simulation make these tools unfeasible in use as design or screening tools.
2. They are too complex, often requiring extended understanding of theoretical molecular thermodynamics, force fields and simulation details that lie outside the domain of expertise of product developers.
3. They are expensive. Often priced at 10000-50000 USD in addition to about 50000-10000 USD worth hardware, they are centralized systems used by specialists in simulation.
Introducing MD Darshan
An Open source software, MD Darshan presents molecular simulation software for the experimentalists and product developers (without losing the sophistication or accuracy required by simulations experts – so simulation experts can use them too.

1. Using high speed gaming processors (GPUs), leveraging open source developments such as OpenMM, MD Darshan simulations are 10 times faster, sometimes more. Self-assembly simulations that are benchmarked to take 7-10 days on 4-6 node clusters, take about 8-15 hours on MD Darshan

2. MD Darshan can be used by a specialist for sophisticated simulations, or new research into molecular dynamics of materials. Alternatively, it can be customized for ready use in product
formulation, or screening of candidates for a variety of applications.

3. MD Darshan is targeted to wide use by product developers and hence is designed to run on a single desktop or laptop that contains certain classes of graphics cards (see hardware specs). These can be bought from standard desktop or laptop manufacturers at 1000-4000 USD.

The software provides modules that allow you to build a library of molecules that are of interest, set them up to design systems or screen candidates for a wide variety of applications, run simulations and visualize and analyze results. It allows you to design new systems, analyze their stability, and test their properties.

MD Darshan is now officially available on github - the repository of most open source software where version control is available. You can access it from https://github.com/okpatil4u/MD-Darshan The software is free. You can download it. We only ask that you give credit to Omkar Patil and Sanat Mohanty when you use it or share results based on MD Darshan. Instructions and the GPL license are also available at the site.

Potential design systems include: polymer systems, solutions, emulsion systems, crystals, coatings and specialized surfaces, and wide variety of nano-structures. Simulations can be run to model assembly, aggregation or order formation or formation of different structures, stability of systems, dynamic analysis such as diffusion, dissolution of crystals or other structures, response to different stresses and small changes in structure under stress. These applications are of interest to industries or labs engaged in study of emulsions, paints, lotions, polymer formulations, adhesives, glues, composites, coatings, drug formulations, and their testing.

Additional Technical Information

Molecular Dynamics Simulations using GPU: MD Darshan has employed highly parallel molecular modeling algorithms that leverage GPU computing making it highly efficient molecular dynamics simulation package.

Forcefields Supported : MD Darshan currently supports Dreiding forcefield with Gasteiger Charge Distribution for modeling and simulation of organic, biological and main-group inorganic molecules. The philosophy in DREIDING is to use general force constants and geometry parameters based on simple hybridization considerations, rather than individual force constants and geometric parameters that depend on the particular combinations of atoms involved in the bond, angle, or torsion terms. For water based simulations, MD Darshan supports TIP3P water model

Supported Operating Systems : Being a cross platform software, MD Darshan can run on Windows, Mac OS or Linux platform.

Compatible Hardware : Intel 2nd Gen Core i7 Processor, 8 GB RAM, 1 GB Free Hard Disk Space with sany among a host of advanced graphics cards sold by NVIDIA, ATI, and others.