Alternatives to GROMACS
Compare GROMACS alternatives for your business or organization using the curated list below. SourceForge ranks the best alternatives to GROMACS in 2026. Compare features, ratings, user reviews, pricing, and more from GROMACS competitors and alternatives in order to make an informed decision for your business.
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1
SYNTHIA Retrosynthesis Software
Merck KGaA
Expert-coded by chemists and engineered by computer scientists, SYNTHIA™ Retrosynthesis Software enables scientists to quickly find and easily navigate innovative and novel pathways for novel and published target molecules. Quickly and efficiently scan hundreds of pathways to help you identify the best option according to your needs. Explore the most cost-effective routes to your target molecules with state of the art visualization and filtering options. Easily customize search parameters to eliminate or promote reactions, reagents or classes of molecules. Explore unique and innovative syntheses that may be unknown for building your desired molecule. Easily generate a list of commercially available starting materials for your synthesis. Benefit from ISO/IEC 27001 Information Security Certification to guarantee the confidentiality, integrity, and protection of your data.Starting Price: €0 / 30 days -
2
ESPResSo
ESPResSo
ESPResSo, the Extensible Simulation Package for Research on Soft Matter, is a highly versatile open source simulation package for performing and analyzing scientific molecular dynamics and Monte Carlo many-particle simulations. It is designed as a universal tool for simulating a variety of soft matter systems, especially coarse-grained atomistic or bead-spring models used in physics, chemistry, molecular biology, and process engineering. ESPResSo can be used to simulate polymers, liquid crystals, colloids, polyelectrolytes, ferrofluids, gels, biological systems, DNA, lipid membranes, bacterial motion, and super-capacitors. In coarse-grained models, a group of atoms or molecules is treated as a single bead, allowing researchers to investigate larger time and length scales than would be practical with fully atomistic simulations. ESPResSo supports classical molecular dynamics simulations in different statistical ensembles.Starting Price: Free -
3
NAMD
Theoretical and Computational Biophysics Group
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, it scales from desktop and laptop computers to high-end parallel platforms, hundreds of cores for typical simulations, and beyond 500,000 cores for the largest simulations. NAMD is built for researchers who need to simulate large molecular systems efficiently while preserving compatibility with widely used molecular modeling workflows. It uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, and it is file-compatible with AMBER, CHARMM, and X-PLOR. It is designed to support biomolecular simulations involving proteins, membranes, nucleic acids, solvents, ions, and other molecular systems where atomic interactions and time-dependent motion need to be studied in detail.Starting Price: Free -
4
LAMMPS
LAMMPS
LAMMPS, the Large-scale Atomic/Molecular Massively Parallel Simulator, is a classical molecular dynamics code with a focus on materials modeling. It models ensembles of particles in liquid, solid, or gaseous states and can simulate atomic, polymeric, biological, solid-state, granular, coarse-grained, mesoscopic, or macroscopic systems using many interatomic potentials, force fields, and boundary conditions. LAMMPS can model systems in two or three dimensions, from only a few particles up to billions, and is designed to run efficiently on parallel computers while remaining easy to extend and modify. It includes potentials for solid-state materials such as metals and semiconductors, soft matter such as biomolecules and polymers, and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generally, as a parallel particle simulator at atomic, meso, or continuum scale.Starting Price: Free -
5
MercuryDPM
MercuryDPM
MercuryDPM is an open source code for discrete particle simulations, designed to simulate the motion of particles or atoms by applying forces and torques from external body forces, such as gravity or magnetic fields, and from particle interaction laws. For granular particles, these forces are typically contact forces, including elastic, plastic, viscous, and frictional interactions, while molecular simulations can use interaction potentials such as Lennard-Jones. MercuryDPM is written as a versatile, object-oriented C++ code and is built to be understandable, flexible, and extensible for researchers and engineers who need to create new simulation models. It is developed extensively for granular applications, while remaining adaptable to other particle-based systems and long-range interactions. Its documentation guides users through installation, running simulations, visualization, analysis, and creating new MercuryDPM codes to model systems of their choice.Starting Price: Free -
6
LIGGGHTS
CFDEM
LIGGGHTS is an open source Discrete Element Method particle simulation tool for modeling particulate materials, with a focus on industrial granular and granular heat-transfer simulations. LIGGGHTS stands for “LAMMPS improved for general granular and granular heat transfer simulations,” and it builds on the LAMMPS molecular dynamics platform to extend DEM capabilities toward practical industrial applications. It can be used to simulate systems where material behavior emerges from the motion, collision, friction, cohesion, heat transfer, and interaction of individual particles. It is suitable for analyzing powders, grains, bulk solids, particulate flows, packed beds, conveying systems, mixing processes, hopper discharge, material handling, and other granular systems where particle-scale behavior matters. LIGGGHTS is currently used by research institutions and companies worldwide for the simulation of particulate materials, especially where open source flexibility.Starting Price: Free -
7
Ansys Rocky
Ansys
Ansys Rocky is a particle dynamics simulation software that uses the discrete element method (DEM) to model and analyze the behavior of granular materials and particle flows. The platform enables engineers to simulate realistic particle shapes, including non-spherical particles, fibers, shells, and complex material interactions. Ansys Rocky leverages multi-GPU processing technology to accelerate large-scale simulations while maintaining high levels of accuracy. The software includes advanced capabilities such as wear prediction, particle breakage modeling, cohesion analysis, CFD coupling, FEA coupling, and multibody dynamics simulation. Engineers can use the platform to study particle movement, material handling, mixing, separation, and equipment performance across a wide range of industries. -
8
PFC (Particle Flow Code)
ITASCA Consulting
PFC, or Particle Flow Code, is a general-purpose distinct-element modeling framework available as two- and three-dimensional programs, PFC2D and PFC3D. It is designed to simulate synthetic granular and solid materials as assemblies of variably sized rigid particles, including disks, spheres, rigidly connected clumps, and convex polygons or polyhedra. It provides an efficient and flexible way to model the motion, interaction, breakage, flow, deformation, and failure of particle systems across geomechanics, mining, civil engineering, materials processing, and industrial design. PFC is especially useful for problems where the behavior of a material emerges from particle-level contacts, bonding, friction, rearrangement, fracture, or flow rather than from a continuous mesh. Users can represent bonded materials such as rock, concrete, or cemented soil, as well as loose granular materials such as sand, gravel, ballast, ore, powders, and grains.Starting Price: $9,588 one-time payment -
9
Aspherix
DCS Computing
Aspherix is a state-of-the-art Discrete Element Method platform designed to simulate particle behavior in diverse systems and provide high-precision process modeling for industrial and research applications. It offers comprehensive DEM simulation tools for analyzing granular materials, powders, bulk solids, cohesive particles, polydisperse materials, and particle interactions across a wide range of environments and processes. Aspherix gives users strong control over simulation data, integrates information from multiple sources, and supports seamless analysis across varied formats, helping teams optimize operations and drive product innovation through data-driven simulation. With user-friendly dashboards and real-time analytics, the platform helps engineers move from complex particle behavior to fast, actionable insights. -
10
XPS (eXtended Particle Simulations)
InSilicoTrials
XPS, or eXtended Particle Simulations, is a state-of-the-art Discrete Element Method simulation software developed by RCPE and distributed globally by InSilicoTrials for high-fidelity particle-based process simulation. Designed specifically for pharmaceutical applications, XPS accurately predicts powder and granular behavior, helping teams better understand, predict, and control pharmaceutical unit operations. It relies on advanced contact models to describe the flow behavior of granular materials and uses massively parallel algorithms optimized for modern GPUs to accelerate simulations, including simulations with up to 100 million particles. XPS helps pharmaceutical engineers assess process configurations in unprecedented detail, explore decision space virtually, reduce costly and time-consuming physical experiments, and support data-driven process development. -
11
Particleworks
Prometech Software
Particleworks is particle-based CAE and CFD software for simulating liquid and multiphase flows using the Moving Particle Simulation method. Its mesh-less solver and intuitive interface make the simulation process simple and fast, even for complex geometries with moving parts such as transmissions, electric motors, internal combustion engines, and other industrial systems. Unlike conventional mesh-based CFD, Particleworks discretizes the fluid domain automatically with particles, eliminating complex mesh generation and making it easier to analyze free-surface flow, splashing, sloshing, spraying, mixing, lubrication, cooling, oil behavior, water interaction, and highly viscous fluids. It provides one-stop GUI operation from pre-processing through post-processing, helping engineers set up models, run simulations, visualize results, and evaluate performance in a streamlined workflow. -
12
Samadii Multiphysics
Metariver Technology Co.,Ltd
Metariver Technology Co., Ltd. is developing innovative and creative computer-aided engineering (CAE) analysis S/W based on the latest HPC technology and S/W technology including CUDA technology. We will change the paradigm of CAE technology by applying particle-based CAE technology and high-speed computation technology using GPUs to CAE analysis software. Here is an introduction to our products. 1. Samadii-DEM (the discrete element method): works with the discrete element method and solid particles. 2. Samadii-SCIV (Statistical Contact In Vacuum): working with high vacuum system gas-flow simulation. Using Monte Carlo simulation. 3. Samadii-EM (Electromagnetics): For full-field interpretation 4. Samadii-Plasma: Plasma simulation for Analysis of ion and electron behavior in an electromagnetic field. 5. Vampire (Virtual Additive Manufacturing System): Specializes in transient heat transfer analysis. additive manufacturing and 3D printing simulation software -
13
iGRAF
iGRAF
iGRAF is an integrated powder and multiphase flow simulation tool that seamlessly merges the domains of powder and fluid simulation. It is designed as a one-stop solution for replicating a wide variety of powder behaviors and redefining standards in simulation technology. iGRAF’s integrated DEM-CFD solver enables accurate and efficient analysis of single-phase and multiphase flow, helping users understand particle-fluid interactions in one platform. Its dynamic geometry control supports translations, rotations, vibrations, and user-defined motion, allowing teams to precisely capture the dynamics of complex systems. It includes validated liquid bridging models and van der Waals forces to analyze the influence of moisture and adhesion on particle behavior, with its liquid bridge force model extensively validated up to 15% moisture content. iGRAF also combines the Signed Distance Function and Immersed Boundary Method to recognize arbitrary solid geometries. -
14
Simcenter EDEM
Siemens
Simcenter EDEM is a high-performance Discrete Element Method tool for bulk material and particle simulation, designed to give engineers crucial insight into how granular materials interact with handling equipment across a range of operating and process conditions. It accurately simulates and analyzes the behavior of coal, ores, soils, fibers, grains, tablets, powders, rocks, crops, and other real-world materials. Users can get started quickly with extensive pre-calibrated material model libraries representing rocks, ores, soils, and powders, while validated physics models support dry, sticky, compressible, and more complex material behaviors. Simcenter EDEM can simulate complex, industry-scale particle systems involving many millions of particles with fast and scalable compute performance across CPU, GPU, and multi-GPU solvers. -
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AWS Thinkbox Stoke
Amazon
Create particle simulations faster for Autodesk 3ds Max compared to competing fluid dynamics plugins. Allow artists without programming or scripting experience to easily use an extensible procedural geometry modifier. Give users access to artist-friendly channel-editing workflows similar to node-based image-compositing applications. Access-optimized geometry and particle lookup operations are not available in the Autodesk 3ds Max SDK. AWS Thinkbox Stoke simplifies and accelerates the creation of high-volume particle clouds. Enable formats, such as PRT and RealFlow BIN, and simulations from FumeFX, Particle Flow, cebas thinkingParticles, and 3ds Max Force Space Warps. Create and simulate new fields, including velocity fields, and the loading and saving of field data using industry-standard formats. Combine field data with 3ds Max subsystems, such as Particle Flow, MassFX, Hair and Fur, Materials, most renderers, and other systems. -
16
Yade
Yade
Yade is an extensible open source framework for discrete numerical models, focused on the Discrete Element Method. Its computation parts are written in C++ using a flexible object model that allows independent implementation of new algorithms and interfaces, while Python is used for rapid and concise scene construction, simulation control, postprocessing, and debugging. Yade is designed for researchers and engineers who need to create, run, inspect, modify, and extend particle-based simulations through scripts, interactive commands, graphical tools, and reusable simulation components. Simulations can be built from specialized generators or constructed directly with Python scripts, giving users flexibility for developing custom models, importing geometries, reusing code, and controlling the full simulation loop. It represents each simulation as a scene containing bodies, interactions, and resultant forces, with bodies defined by geometry, material properties, state variables, etc.Starting Price: Free -
17
Ascalaph Designer
Agile Molecule
Ascalaph Designer is a general-purpose program for molecular dynamic simulations. Under a single graphical environment are represented as their own implementation of molecular dynamics as well as the methods of classical and quantum mechanics of popular programs. Molecular geometry optimization with conjugate gradient methods. Shows molecular models in separate windows. Each window has two cameras, which allow the model to be simultaneously visualized from two sides and in different graphic modes. The subwindow can be opened by dragging the splitter in the right corner of each graphical window. Clicking on an atom or bond with the left mouse button slightly changes their color and a brief info about the picked object appears in the status bar. The wire-frame style is convenient for large molecules, particularly, proteins. Drawing is very fast for this style. Finally, CPK wire frame combines the properties of several above styles.Starting Price: Free -
18
MFiX
National Energy Technology Laboratory
MFiX, or Multiphase Flow with Interphase eXchanges, is an open source multiphase flow solver and NETL’s flagship suite of computational fluid dynamics tool for modeling reacting multiphase flows. It has become a standard for comparing, implementing, and evaluating multiphase flow constitutive models, and has been applied to a diverse range of multiphase flow devices and industrial systems. MFiX provides multiple modeling approaches, including a Two-Fluid Model, Discrete Element Model, Coarse-Grained Particle DEM, Superquadric Particle DEM, Glued-Sphere Particle DEM, Particle-in-Cell model, hybrid methods, and a single-phase solver for pure granular flows. These models can be used to simulate gasifiers, circulating fluidized bed combustors, fluidized beds, fluid catalytic crackers, chemical looping combustion systems, and other particle-fluid systems involving hydrodynamics, heat transfer, species transport, and chemical reactions.Starting Price: Free -
19
Trapcode Suite
Maxon
Trapcode Suite brings the power of 3D particle systems right into After Effects. Use particle emitters to create fire, water, smoke, snow and other organic visual effects, or create technological marvels and user interfaces with immortal particle grids, text and 3D forms. Combine multiple particle systems into one unified 3D space and design emitters that emit full emitters for creating visually stunning results. With GPU acceleration, Trapcode plugins help you get beautiful results fast. Trapcode Suite includes a physics engine with powerful behaviors, forces and environmental controls. Particular brings particles to life with new flocking/swarming and predator/prey behaviors, and adds more realism with combined bounce and air physics. Particular and form both include the ability to create organic fluid simulations where particle systems interact with beautiful results.Starting Price: $49.91 per month -
20
YASARA
YASARA
YASARA is a molecular graphics, modeling, and simulation program for Windows, Linux, MacOS, and Android developed in 1993, that finally makes it really easy to answer your questions. With an intuitive user interface, photorealistic graphics, and support for affordable virtual reality headsets, shutter glasses, autostereoscopic displays, and input devices, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program. YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software. PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs, making use of GPUs if available. You can push and pull molecules around and work with dynamic models instead of static pictures.Starting Price: Free -
21
BIOVIA Discovery Studio
Dassault Systèmes
Today’s biopharmaceutical industry is marked by complexity: growing market demands for improved specificity and safety, novel treatment classes and more intricate mechanisms of disease. Keeping up with this complexity requires a deeper understanding of therapeutic behavior. Modeling and simulation methods provide a unique means to explore biological and physicochemical processes down to the atomic level. This can guide physical experimentation, accelerating the discovery and development process. BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment. It provides researchers with a complete toolset to explore the nuances of protein chemistry and catalyze discovery of small and large molecule therapeutics from Target ID to Lead Optimization. -
22
Bulk Flow Analyst
Overland Conveyor Company
Bulk Flow Analyst is a Discrete Element Method simulation tool designed to help engineers analyze and optimize bulk material flow throughout transfer chutes and conveyor systems. Developed and used by engineers with direct expertise in transfer chute design, the software is built to make DEM simulation intuitive and practical so users can focus on chute performance instead of managing complex DEM parameters. Bulk Flow Analyst can simulate transfer problems involving bulk materials moving through chutes, hoppers, feeders, conveyor transfer points, belts, and related material-handling equipment. It helps designers visualize and evaluate how particles flow, impact, accumulate, discharge, and interact with geometry under different operating conditions. Through DEM, it supports analysis of difficult conveyor design challenges such as flow requirements, chute plugging, belt wear, chute surface wear, dust generation, spillage, material degradation, and impact behavior.Starting Price: $1,000 one-time payment -
23
Avogadro
Avogadro
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Avogadro is a free, open-source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. -
24
X-Particles
INSYDIUM
Create outstanding ParticleFX from Solar Systems, FUI, Holograms and medical visualizations to abstract artwork. Multiple options to combine Emitters and Modifiers, gives you a range of possibilities. Realistic smoke, fire and explosive simulations. You can export ExplosiaFX as a VDB volume, and any render engine that can read the VDB data can then render the volume data. Our Liquid and Grain Solvers enable you to create stunning large and small-scale fluid simulations. From gorgeous beaches, with waves and ocean spray, to beautiful product shot splashes. Drive Cloth simulations with any Modifier, then rip it apart with the advanced tearing options. ClothFX adds a whole new dimension to motion design effects and destruction VFX shots. -
25
RecurDyn
FunctionBay
RecurDyn is an interdisciplinary computer-aided engineering software package whose primary function is the simulation of Multi-Body Dynamics. It simulates both rigid and flexible body dynamics by combining traditional rigid multibody dynamics with cutting-edge finite element technology for modeling flexible bodies, known as Multi Flexible Body Dynamics. RecurDyn is designed to analyze the dynamic behavior of mechanical systems in motion, including systems with joints, constraints, contact, flexible components, forces, and complex interactions between parts. Its solver technology handles the differential algebraic equations that describe multibody systems, combining equations of motion with algebraic equations for joint constraints. It provides a robust MBD-specialized modeling environment, fast solvers, extensive post-processing, animation, plotting, and tools for evaluating the motion, loads, stresses, deformation, and performance of mechanical assemblies. -
26
Promethium
Promethium
Promethium is a GPU-powered chemistry simulation platform designed to accelerate drug and materials development by enabling faster and more accurate quantum chemistry calculations. Built from the ground up for NVIDIA datacenter GPUs like A100, it employs novel QC Ware streaming algorithms to achieve unprecedented computational speed and high throughput-to-power consumption ratios. It supports density functional theory calculations on systems with up to 2,000 atoms, allowing simulations of large molecular systems that are not feasible with legacy CPU-powered ab initio codes. For instance, a single-point calculation of a 2,056-atom protein can be completed in 14 hours on a single GPU. Promethium offers a range of capabilities, including single-point energy calculations, geometry optimization, conformer search, torsion scan, reaction path optimization, transition state optimization, interaction energy computations, and relaxed potential energy surface scans.Starting Price: $30 per hour -
27
HyperProtein
Hypercube
HyperProtein is Hypercube, Inc.'s new product focusing on the computational science associated with protein sequences. The product includes the analysis of one-dimensional protein sequences as well as the analysis of consequent three-dimensional protein structures. In particular, the relationship between sequence and structure is a fundamental facet of the product. Unlike individual software programs that provide capability for some aspect of protein sequence or structure, such as sequence alignment, HyperProtein puts together a multitude of Bioinformatics and Molecular Modeling tools related to the science that initiates with a protein sequence. -
28
BIOVIA
Dassault Systèmes
BIOVIA solutions create an unmatched scientific management environment that can help science-based organizations create and connect biological, chemical and material innovations to improve the way we live. The industry-leading BIOVIA portfolio is focused on integrating the diversity of science, experimental processes and information requirements end-to-end across research, development, QA/QC and manufacturing. Capabilities over the areas of Scientific Informatics, Molecular Modeling/Simulation, Data Science, Laboratory Informatics, Formulation Design, BioPharma Quality & Compliance and Manufacturing Analytics. BIOVIA is committed to enhancing and speeding innovation, increasing productivity, improving quality and compliance, reducing costs and accelerating product development for customers in multiple industries. Manage and connect scientific innovation processes and information across the product lifecycle. -
29
alvaBuilder
Alvascience
alvaBuilder is a no-code de novo molecular design software for generating novel chemical structures that satisfy user-defined structural, physicochemical, and modeling constraints. It enables the creation of new molecules starting from scratch or by evolving existing structures using fragment-based and rule-driven approaches. alvaBuilder integrates seamlessly with QSAR/QSPR workflows, allowing users to guide molecule generation using predictive models, descriptor ranges, and property targets. The software supports medicinal chemistry, lead optimization, and virtual screening tasks by efficiently exploring chemical space while maintaining chemical feasibility and interpretability. alvaBuilder is designed for research and industrial applications where transparent, controllable, and reproducible molecular generation is required. -
30
Swiss-PdbViewer
Swiss-PdbViewer
Swiss-PdbViewer (aka DeepView) is an application that provides a user-friendly interface allowing to analysis of several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles, and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Swiss-PdbViewer (aka DeepView) has been developed since 1994 by Nicolas Guex. Swiss-PdbViewer was initially tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel. However, the SWISS-MODEL web interface evolved to a point where it is now possible to use it directly for advanced modeling. Maintaining a direct interface with Swiss-PdbViewer is too complex and no longer supported. -
31
INSYDIUM Fused
INSYDIUM
INSYDIUM Fused contains all of our plugins and products in one complete collection. Everything you need to create stunning particle effects, realistic terrains and fulfil modeling tasks through to the final render. Plus, all our available 3D resources, hours of training, technical support, and content repository files. Get your copy of INSYDIUM Fused, which includes X-Particles, the ultimate particle engine for Cinema 4D, TerraformFX, Mesh Tools, Cycles 4D and much more. An essential component of an artist’s toolkit, X-Particles is the solution to satisfy all your particle needs, cloth, smoke, fire, fluids, grains and dynamics. Designers can switch effortlessly between motion graphics and VFX, within a unified system. Create outstanding ParticleFX from solar systems, FUI, holograms and medical visualizations to abstract artwork. Multiple options to combine emitters and modifiers, gives you a range of possibilities.Starting Price: $188.34 per 3 months -
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Ansys Autodyn
Ansys
Simulate the response of materials to events ranging from short duration severe mechanical loadings, high pressures and even explosions. Ansys Autodyn provides advanced solution methods without compromising ease of use. Ansys Autodyn makes it easy to quickly understand and simulate large material deformation or failure. Autodyn has a range of models to represent complex physical phenomena such as the interaction of liquids, solids and gases; the phase transitions of materials; and the propagation of shock waves. By Integrating within Ansys Workbench and its own native-user interface, Ansys Autodyn has long led the industry in ease of use, enabling you to produce accurate results with the least amount of time and effort. The smooth particle hydrodynamics (SPH) solver completes the picture to provide everything needed for explicit analysis. Ansys Autodyn lets you select from different solver technologies so the most effective solver can be used for a given part of the model. -
33
NVIDIA BioNeMo
NVIDIA
BioNeMo is an AI-powered drug discovery cloud service and framework built on NVIDIA NeMo Megatron for training and deploying large biomolecular transformer AI models at a supercomputing scale. The service includes pre-trained large language models (LLMs) and native support for common file formats for proteins, DNA, RNA, and chemistry, providing data loaders for SMILES for molecular structures and FASTA for amino acid and nucleotide sequences. The BioNeMo framework will also be available for download for running on your own infrastructure. ESM-1, based on Meta AI’s state-of-the-art ESM-1b, and ProtT5 are transformer-based protein language models that can be used to generate learned embeddings for tasks like protein structure and property prediction. OpenFold, a deep learning model for 3D structure prediction of novel protein sequences, will be available in BioNeMo service. -
34
QSimulate
QSimulate
QSimulate offers a suite of quantum simulation platforms that leverage quantum mechanics to solve complex, industrial-scale problems in life sciences and materials science. The QSP Life platform provides unique quantum-powered methods for drug discovery and optimization, enabling first-of-a-kind quantum simulations of ligand-protein interactions applicable throughout the computational drug discovery process. The QUELO platform performs hybrid quantum/classical free energy calculations, offering users the ability to run relative free energy calculations using the free energy perturbation (FEP) approach. Additionally, QSimulate's technology enables groundbreaking advances in quantum mechanics/molecular mechanics (QM/MM) simulations for large protein modeling. For materials science, the QSP Materials platform democratizes quantum mechanical simulations, allowing experimentalists to automate complex workflows without the need for specialization. -
35
Evo 2
Arc Institute
Evo 2 is a genomic foundation model capable of generalist prediction and design tasks across DNA, RNA, and proteins. It utilizes a frontier deep learning architecture to model biological sequences at single-nucleotide resolution, achieving near-linear scaling of compute and memory relative to context length. Trained with 40 billion parameters and a 1 megabase context length, Evo 2 processes over 9 trillion nucleotides from diverse eukaryotic and prokaryotic genomes. This extensive training enables Evo 2 to perform zero-shot function prediction across multiple biological modalities, including DNA, RNA, and proteins, and to generate novel sequences with plausible genomic architecture. The model's capabilities have been demonstrated in tasks such as designing functional CRISPR systems and predicting disease-causing mutations in human genes. Evo 2 is publicly accessible via Arc's GitHub repository and is integrated into the NVIDIA BioNeMo framework. -
36
Khimera
Kintech Laboratory
Khimera is used to calculate the kinetic parameters of microscopic processes, thermodynamic and transport properties of substances and their mixtures in gases, plasmas and gas-solid phases boundary. The primary users are researchers and engineers, involved in kinetic model development as well as thermodynamic and kinetic modeling for chemical engineering, combustion, catalysis, metallurgy, and microelectronics areas. Khimera ideally fits the needs of multi-scale modeling providing the link between fundamental molecular properties of individual molecules and mesoscale ensemble-averaged characteristics of the reactive medium: thermodynamic and transport properties as well as rates of chemical reactions. All the models can use the results of quantum-chemical simulations as an input, thus providing the possibility to recover properties without any experimental input from the user side. -
37
BIOVIA Materials Studio
Dassault Systèmes
BIOVIA Materials Studio is a comprehensive modeling and simulation environment designed to enable researchers in materials science and chemistry to predict and understand the relationships between a material’s atomic and molecular structure and its properties and behavior. Utilizing an "in silico first" approach allows for the optimization of material performance in a cost-effective virtual setting prior to physical testing. It supports a wide range of materials, including catalysts, polymers, composites, metals, alloys, pharmaceuticals, batteries, and more. It offers tools for quantum, atomistic, mesoscale, statistical, analytical, and crystallization simulations, facilitating the design of advanced materials across various industries. Features include the ability to accelerate innovation, reduce R&D costs through virtual screening, and improve efficiency by automating best practices within Pipeline Pilot. -
38
Schrödinger
Schrödinger
Transform drug discovery and materials research with advanced molecular modeling. Our physics-based computational platform integrates differentiated solutions for predictive modeling, data analytics, and collaboration to enable rapid exploration of chemical space. Our platform is deployed by industry leaders worldwide for drug discovery, as well as for materials science in fields as diverse as aerospace, energy, semiconductors, and electronics displays. The platform powers our own drug discovery efforts, from target identification to hit discovery to lead optimization. It also drives our research collaborations to develop novel medicines for critical public health needs. With more than 150 Ph.D. scientists on our team, we invest heavily in R&D. We’ve published over 400 peer-reviewed papers that demonstrate the strength of our physics-based approaches, and we’re continually pushing the limits of computer modeling. -
39
ChemSketch
ACD/Labs
Comprehensive molecular structure drawing and naming. Draw chemical structures and communicate your science. -
40
MolPad
MolPad
MolPad integrates an interactive chemistry sketcher into any online learning platform. Build open questions about molecular structure and organic chemistry that go beyond just recognizing the right answer. Discover how MolPad can enrich online chemistry education by providing a low code environment for creating dynamic content and smart assessment. With MolPad, we have developed several solutions for interactive and intuitive drawing of structural formulas, enabling the student to practice with topics like chemical naming, functional groups, and Lewis structures in a digital environment. By providing smart feedback based on specific errors, the student can gain more insight than with multiple choice questions. -
41
alvaModel
Alvascience
alvaModel is a software tool for building, validating, comparing, and applying QSAR and QSPR models. It supports regression and classification workflows based on molecular descriptors and fingerprints, with a strong focus on model transparency, interpretability, and scientific robustness. The software includes multiple data splitting strategies, variable selection methods, modeling algorithms, and comprehensive internal and external validation procedures. alvaModel provides diagnostic plots, applicability domain analysis, and model comparison tools to support the identification of reliable and predictive models. Designed according to best practices in chemometrics, alvaModel facilitates the development of interpretable models consistent with the OECD principles for QSAR validation, making it suitable for research and regulatory-oriented applications. The graphical interface guides users through the entire modeling workflow while allowing full control over each modeling step. -
42
Evo Designer
Arc Institute
Evo Designer is an advanced tool developed by the Arc Institute, leveraging the capabilities of the Evo 2 genomic foundation model to facilitate DNA sequence generation and analysis. This platform enables users to input nucleotide sequences or specify organisms, prompting the model to generate corresponding DNA sequences. It provides comprehensive annotations of coding regions and, for prokaryotic sequences, offers 3D protein visualizations utilizing ESMFold. Additionally, Evo Designer evaluates sequences by scoring their perplexity and per-nucleotide entropy, assisting researchers in assessing sequence complexity and variability. The underlying Evo 2 model is trained on over 9 trillion nucleotides from a diverse array of prokaryotic and eukaryotic genomes, employing a deep learning architecture that models biological sequences at single-nucleotide resolution with a context window extending up to 1 million tokens. -
43
Red Giant Complete
Maxon
Get up-to-speed with all the latest features in Red Giant Complete. Trapcode brings the power of 3D particle systems right into After Effects. Use particle emitters to create fire, water, smoke, snow and other organic visual effects, or create technological marvels and user interfaces with immortal particle grids and 3D forms. With a subscription to Red Giant, get even more 3D geometry input options thanks to Cineware .c4d file import. Use Cinema 4D files (including animation) in particle systems or as 3D models in After Effects. Magic Bullet is a set of plugins for color correction, finishing and film looks. With powerful real-time color grading tools, video denoising, and cosmetic retouching, you’ll have everything you need to make your footage look great, right on your editing timeline. Universe is a set of video transition and effects plugins for editors and motion graphics artists.Starting Price: $49.91 per month -
44
Tox Suite
ACD/Labs
Calculate drug toxicity and safety endpoints to reduce attrition rates of molecular entities that are unlikely to succeed to nomination as a drug candidate, direct new compound synthesis, and focus animal testing requirements. -
45
PyMOL
PyMOL
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. PyQt interface replaces Tcl/Tk and MacPyMOL on all platforms. Better third-party plugin and custom scripting support. A comprehensive software package for rendering and animating 3D structures. A plug-in for embedding 3D images and animations into PowerPoint presentations. PyMOL is a commercial product, but we make most of its source code freely available under a permissive license. The open-source project is maintained by Schrödinger and ultimately funded by everyone who purchases a PyMOL license. Open access incentive executables. Liberal evaluation policy. Improved fuse command (disallows hypervalent bonds, substitutes monovalent atoms instead of attaching to them) Properties inspector now supports unsetting settings with the “delete” key. Fix workspace disappearing on specific display resolutions. -
46
MoluCAD
New River Kinematics
MoluCAD is a full-featured molecular modeling and visualization tool designed for Windows. It is the result of a three-year National Institutes of Health biomedical technology research project aimed at producing low-cost educational software for chemistry students. The latest version incorporates many advanced features only found in expensive workstation-based modeling packages. Ease of use, premium graphical quality, and computational robustness are the trademarks of MoluCAD. Novice users are able to quickly generate models, view them form any perspective, create reaction animations, and save all data to disk. -
47
COMSOL Multiphysics
Comsol Group
Simulate real-world designs, devices, and processes with multiphysics software from COMSOL. General-purpose simulation software based on advanced numerical methods. Fully coupled multiphysics and single-physics modeling capabilities. Complete modeling workflow, from geometry to postprocessing. User-friendly tools for building and deploying simulation apps. The COMSOL Multiphysics® software brings a user interface and experience that is always the same, regardless of engineering application and physics phenomena. Add-on modules provide specialized functionality for electromagnetics, structural mechanics, acoustics, fluid flow, heat transfer, and chemical engineering. Choose from a list of LiveLink™ products to interface directly with CAD and other third-party software. Deploy simulation applications with COMSOL Compiler™ and COMSOL Server™. Create physics-based models and simulation applications with this software platform. -
48
Miarmy
Basefount
Miarmy (read My Army) is a human logic engine-based Maya plugin for crowd simulation, AI & behavioral animation, creature physical simulation, and rendering. Miarmy simulator is free forever. You can download the full software package, along with tons of tutorials, samples, demo files, and documents. We also provide some official samples and ready-to-run presets. And the most amazing part is, they are totally free. Create stunning crowd VFX using Maya particles, field, fluid, and transform. Support standard production pipeline, reference, and motion builder. Build a human fuzzy logic network without any programming or node connecting.Starting Price: $1,350 per year -
49
CentiLeo
CentiLeo
Fast and easy to use GPU path tracer. CentiLeo is a fast GPU renderer integrated with 3ds Max and Cinema 4D supporting GPU VRAM software extension and with high efficiency for scenes with complex lighting. For 3ds Max and Cinema 4DCentiLeo is an offline GPU renderer with very fast unbiased path tracing for complex lighting. It supports huge scene assets with GPU-accelerated out-of-core technology that effectively renders the polygon counts, particles and textures that may not fit entirely to GPU memory. This feature extends GPU memory limits for geometry/particles by 4x and for texture memory limits by 100x. CentiLeo supports Interactive Preview Render, node-based material & shader editing, displacement mapping, motion blur, subsurface scattering, fast noise reduction for multi-materials, glass objects and mesh lights. CentiLeo is supported by Skolkovo Foundation, some of software R&D results were supported by Skolkovo grants. -
50
ArgusLab
ArgusLab
ArgusLab is a molecular modeling, graphics, and drug design program for Windows operating systems. It’s getting a little dated by now, but remains surprisingly popular. To date, there are more than 20,000 downloads. ArgusLab is freely licensed. You don’t need to sign anything. You can use as many copies as you need if you are teaching a class where your students might benefit from using ArgusLab. You are not allowed to redistribute ArgusLab from other websites or sources. However, you may link to this website from your own websites if you like. A low-key effort is currently underway to port ArgusLab to the iPad. In addition, I’ve done some work with the Qt cross-platform development environment in an effort to support Mac, PC, and Linux.Starting Price: Free
