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計算化学ソフトウェア

GRRM20

GRRM is a code to perform a local, semiglobal, or global reaction path exploration. It is very useful for many purposes from a conventional reaction path calculation to an exhaustive reaction path exploration and a complex rection path network construction. It has been applied to various reaction systems such as organic reaction, organometallic catalysis, cluster catalysis, radical reaction, photoreaction involving electronic excited states, crystal phase transition under periodic boundary conditions, enzyme catalysis described by QM/MM-ONIOM method, and so on. GRRM includes internal interfaces with Gaussian03/09/16, molpro, GAMESS, ORCA, TURBOMOLE, and SIESTA, and can also be combined with any electronic structure calculation code by preparing a simple code. There are many new features in the version GRRM20, and four major ones are described below.

Overview

Commercial GRRM with a number of new features

▸ Kinetic simulation / kinetics-based navigation using RCMC
▸ Periodic boundary conditions (PBCs)
▸ An optimizer for systems including >500 active atoms
▸ Massive parallelization (simultaneous search for several hundreds of reaction pathways, using MPI)
▸ Speedups
▸ Interface for changing AFIR search method from the outside
▸ Price, Specification and Support
▸ GRRM program function comparison table

See the following references for new features:
S. Maeda, Y. Harabuchi, Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force., WIREs Comput. Mol. Sci., 2021, 11, e1538 (23 pages). https://doi.org/10.1002/wcms.1538

You can see all of the chemical reactions.

With the input of just one molecule, GRRM can automatically explore for all the products that can be produced from them, all the reactants that can produce them, and all their reaction pathways. It can be used in various fields such as catalyst design and material screening.

Input	Output
Input	Number of stable structures (Reactant / Product / Intermediate)	Number of elementary reactions
acetic acid CH₃COOH	121	848
propionic acid C₃H₂O₂	207	1,114
methyl nitrate CH₃NO₃	676	4,835
lactaldehyde C₃H₆O₂	1,366	10,103

Features

Kinetic simulation / kinetics-based navigation using RCMC

A kinetic analysis method, rate constant matrix contraction (RCMC), which is applicable to complex reaction path networks is available in GRRM20. RCMC can be used in two purposes: (1) as a kinetic navigation of the SC-AFIR search, and (2) analysis of a reaction path network obtained by a SC-AFIR search. The kinetic navigation enables to perform an on-the-fly kinetic simulation of a given chemical system under an experimental condition (reaction temperature and reaction time). The latter allows to coarse-grain a reaction path network, to compute an overall rate constant between the reactant and the product, to extract the kinetically most feasible path from a reaction path network, and so on.

Periodic boundary conditions (PBCs)

Geometry optimization, reaction path calculation, and automated reaction path exploration under PBCs are possible in GRRM20. When translational vectors are specified as active, both translational vectors and atom positions are optimized simultaneously. In addition, an automated search for paths of reactions on a 2D/1D slab model can also be performed by fixing all or some of translational vectors.

An optimizer for systems including >500 active atoms

An optimization algorithm for systems including a large number of active variables is available in GRRM20. The algorithm performs a geometry optimization in the full dimension using a limited dimensional PES expressed by gradient vectors obtained during the optimization. Its performance was tested with systems including up to 1000 atoms in combination with a semi-empirical quantum chemical calculation method.

Massive parallelization

In GRRM20, parallelization efficiency of SC-AFIR calculations was improved significantly. Various jobs that execute 100-500 path calculations simultaneously have been done in the developer group. In these jobs, several cores have been used in each path calculation, and thus the total numbers of cores used in these jobs have been 1000~2000.

Speedups

Many fine optimizations and speedups have been made, backed by the state-of-the-art practical achievements of GRRM developers.

Interface for changing AFIR search method from the outside

With a simple external script, you can use the option to reflect informatics methods and empirical rules in the search procedure, and users can also participate in the development of methods for accelerating automatic search.

Applicable for various R&D

For example, drug synthesis. By clarifying all reaction pathways that can synthesize the desired drug molecule, it can be used for catalyst design for rate-determining reactions and suppression of by-products.

For example, designing luminescent materials. Since the stability of the material can be considered from the viewpoint of reaction, it can be used for designing long-life materials that emit stable light.

For example, a combustion reaction. Thousands and tens of thousands of elementary reactions can be obtained based on highly accurate quantum chemistry calculations, so it is possible to meet the accuracy of reaction speed in car and rocket engine design CAE.

Price, Specification and Support

Price

You can purchase an annual (per year) license. For more information, please contact us using this form. When making inquiries, please enter the email address of your organization, not the free email address.

Specification


Operating environment	- Hardware - x86_64 computer that works below - OS - Red Hat Enterprise Linux 7.x or CentOS 7.x Red Hat Enterprise Linux 8.x or CentOS 8.x (Red Hat Enterprise Linux 6.x and CentOS 6.x are not supported.) - Required software - Gaussian16 or Gaussian09 1 - Optional software - Gaussian03, Molpro, GAMESS, ORCA, Turbomole, SIESTA 2 *3
Included items	Software and user manual

*1 Not included in this product. Please prepare in advance.
*2 Not included in this product. If you want to use it, please prepare it in advance.
*3 GRRM20 has the general interface with external ab initio programs.

Support

We support you for troubles in setting up and starting GRRM20 for free of charge.

For how to use GRRM20 and how to interpret the results, please contact the Forum on the AFIR site by yourself. (Please note: when purchasing the GRRM20 license, please register as a user on the AFIR site).

Please refer to the Manual page on the AFIR site for the latest GRRM20 Users Manual.