SCIGRESS

SCIGRESS is a multiplatform molecular design, modeling, and dynamics software suite aimed at experimental chemists working in organic, medicinal, and biochemistry. It provides molecular builders and visualization tools that allow researchers to construct novel structures and calculate chemical and physical properties across multiple theory levels without requiring deep expertise in computational chemistry. The software is intended to support rapid testing of research ideas before wet lab work, reducing time and resource expenditure on failed experiments.

SCIGRESS is distributed by FQS Poland, a subsidiary of Fujitsu Limited, and is available in three editions: SCIGRESS Modeling, SCIGRESS Dynamics, and SCIGRESS Worksystem, each covering different subsets of computational methods and calculation types.

Molecular Building and Visualization

• Integrated, property-oriented GUI for building molecules and larger systems.
• Automated 2D to 3D conversion with hydrogen addition.
• Library of popular organic molecules.
• Protein editor and peptide builder.
• Crystal builder.
• Builders for molecular dynamics systems covering solid state, liquid, amorphous, polymer, liquid crystal, and other system types.
• Molecular editor and visualizer with customizable rendering options.
• Interactive spectra and interactive potential energy graphs.
• Orbital and electronic structural feature visualization.
• Stereoscopic 3D visualization on compatible hardware.

Job Submission and Data Management

• Fully automated job submission, data retrieval, and analysis.
• Local and remote calculations initiated from the interface.
• Multi-step simulations.
• Chemical Spreadsheet for batch jobs and automated QSAR analysis.
• Project explorer for tracking relationships between input and output files.
• Customizable predefined procedures for common calculations.
• PubChem search integration.

Functional Areas

• General Chemistry: geometry building and optimization of small molecules; conformational analysis; electronic property calculations including charges, orbitals, electron density, and reactivity; reaction modeling via transition state search and reaction path calculations; spectroscopy (UV, IR, NMR).
• Biochemistry and Drug Design: import, repair, and optimization of protein structures; compound library screening by docking including quantum docking; building and applying ADMET models with QSAR.
• Materials Science: supported through molecular dynamics builders and associated force fields.

Theory Levels and Computational Methods

• Molecular Mechanics: MM2 and MM3 force fields for preoptimization.
• Quantum Semiempirical: methods including MINDO/3, MNDO, MNDO/d, AM1, PM3, PM5, PM6, RM1, PDDG/MNDO, PDDG/PM3; spectroscopy methods including ZINDO, INDO/S, CNDO/S, CNDO/S2, CNDO/S3, CNDO/1, CNDO/2, INDO/1, INDO/2; solvent effects via COSMO and Onsager models; linear scaling semiempirical methods for protein optimization and docking.
• DFT functionals: D-VWN, D-PW92, B88-PW91, PW91-PW91, B88-P86, B88-LYP.
• Orbital basis sets: 3-21G, 3-21G(p), 6-31G, 6-31G(p), 6-31G(p,d), DZVP, TZVP.
• Molecular Dynamics: over 100 force fields covering organic systems (AMBER, CC, Dreiding, KKY, Klein-McDonald, MM2, MOMEC, OPLS, SPC, TIP), inorganic 2-body potentials (Born-Mayer-Huggins, Erkoc, Johnson, Kawamura, Lennard-Jones, Morse), 3-body potentials (Justo, Marks, Stillinger-Weber, Tersoff), EAM potentials (Ackland, Finnis-Sinclair, Grujicic-Zhou, Oh-Johnson, Rosato-Guillop-Legrand, tight binding, Voter-Chen, Yang-Johnson), and others (CFF, UFF).

External Engine Interfaces

• Amsterdam Modeling Suite (ADF and BAND)
• AutoDock (Tools and Vina)
• CONFLEX
• GAMESS
• Gaussian
• LAMMPS
• MOPAC
• Quantum ESPRESSO

Product Lineup Comparison

• SCIGRESS Modeling includes molecular mechanics, semiempirical methods, DFT, single point and energy calculations, thermodynamic quantities, geometry optimization, conformational analysis, spectroscopy, transition state and reaction searching, protein optimization, simple and multiple/quantum docking, QSAR, PubChem search, and batch calculations. It provides GUI access to Amsterdam Modeling Suite (ADF), AutoDock, CONFLEX, GAMESS, Gaussian, and MOPAC.
• SCIGRESS Dynamics includes molecular mechanics, MD force fields, geometry optimization, advanced molecular dynamics, MD trajectory analysis, and batch calculations. It provides GUI access to Amsterdam Modeling Suite (ADF and BAND), LAMMPS, and Quantum ESPRESSO.
• SCIGRESS Worksystem includes all methods and calculation types available across both Modeling and Dynamics editions, with GUI access to all supported external engines.

Parallel Engines

• Semiempirical methods (MO-G): supported on Windows, Linux, and Server.
• DFT (DGauss): supported on Windows, Linux, Mac, and Server.
• Protein optimization (LocalSCF): supported on Windows, Linux, Mac, and Server.
• Molecular dynamics (MD-ME): supported on Windows, Linux, Mac, and Server.

SCIGRESS runs on Windows 10 and 11 (64-bit), Linux distributions including Ubuntu, RedHat, and CentOS (64-bit), and macOS X 10.9 and higher, with OpenGL accelerated graphics hardware required. Server deployment requires Java Runtime Environment version 7 or 8 and an SSH server for access and file transfer. External compute engines are not distributed with SCIGRESS and must be obtained separately.