Complete Guide to the Fragment Molecular Orbital Method in GAMESS

From One Atom to a Million, at your Service

Dmitri G Fedorov

Natonal Insttute of Advanced Industrial Science and Technology (AIST), Japan

Endorsement

“It is rather tmely to have a rigorous but user-oriented and accessible book for the fragment molecular orbital. The implementaton within GAMESS with a clear descripton of how to invoke FMO optons, practcal tps on how to apply these, and concrete examples will be of great practcal value in addressing computatonal materials problems in biology, chemistry, and physics. A comprehensive treatment of both fundamental and practcal concerns in FMO are included: the use of various levels of quantum chemical theory within FMO, PIEDA, segmentaton and fragmentaton, efectve potentals and grids, and massively scaling up the calculaton size.”

Kang Hway Chuan Associate Professor of Chemistry, Natonal University of Singapore

Key Features

• irst book covering usage o in G ESS

• Uni ue up to date te tbook on rapidl developing methods

• Wri en rom a user perspectve, includes troubleshootng common problems encountered

• Point b point la man descripton o technical ke words

• eep anal sis o per ormance issues arising rom the coarse grained use o CPUs in massivel parallel calculatons

• Supplementar material containing a collecton o input and output fles or G ESS to assist readers in reading the book is provided online

Descripton

The fragment molecular orbital (FMO) method is a fast linear-scaling quantum-mechanical method employed by chemists and physicists all over the world. t provides a wealth o propertes o ragments rom uantum chemical calculatons, a bo omless treasure pit or data mining and machine learning. However, there is no user riendl descripton o its usage in the widel emplo ed uantum chemical open source so ware G ESS, nor is there an book covering the usage o G ESS in general. his leaves ver man interested users to their own devices to get through a variet o problems with ver cr ptc descriptons o ke words in the program manual and no guide whatsoever as to what optons should be set or partcular scientfc tasks. his book is the panacea to man rustratons.

he main ocus o the book is to build a solid bridge connectng users to G ESS, b giving a help ul introducton o various methods as needed or partcular problems ound in computatonal chemistr , and describing in detail how to do these simulatons and understand the results rom the output o the program. he book also covers paralleli aton strategies or a aining high parallel e cienc in massivel parallel computatons, and provides means to anal e per ormance and design a soluton or overcoming per ormance bo lenecks. special secton is devoted to dealing with problems in e ecutng G ESS, arising rom computatonal environment and user errors. inall , 4 care ull selected t pes o applicatons are discussed in detail, describing the input ke words and e plaining where to fnd the main results in the te t based output.

Author

Dr Dmitri G Fedorov is Senior esearcher at the esearch Center or Computatonal esign o dvanced unctonal aterials (C at), atonal nsttute o dvanced ndustrial Science and echnolog ( S ), apan.

February 2023

Imprint: World Scientfc Publishing

Compan

Extent: 300pp

Type: onograph

Main Subject: Chemistr

Sub-Subjects: Computatonal Chemistr Supercomputng Parallel Computng heoretcal Chemistr uantum Chemistr ioin ormatcs iocomputng Computatonal iolog Computatonal anoscience Ph sical Chemistr Computatonal, athematcal nd heoretcal Ph sics uantum echanics nd uantum n ormaton

Keywords: rug esign edicinal Chemistr olecular nteractons uantum Chemistr Linear Scaling ethods High Per ormance Computng Solvent E ects Sur ace dsorpton

Readership: esearch groups in the undamental felds o computatonal chemistr , biolog , ph sics and applied felds o catal sis, drug discover , materials science, both in academia and in industr . Courses on computatonal chemistr biochemistr ph sics (can be used as re erence te tbook). evelopers o theoretcal methods and related scientfc so ware

• Introducton

• Getng Started:

Practcal Summary of FMO

Installaton of GAMESS

Understanding Parallel Executon

How to Run GAMESS

General Structure of GAMESS Input Files

FMO Input Files

FMO result fles (out, dat, trj, rst, and F40)

How to Begin Your Own FMO Calculatons

Parallelizaton Strategy

• Basic FMO Calculatons:

Treatng Solvent

Desolvaton Penalty in Binding (SBA)

Solvent Screening

Polarizaton, Interacton, and Binding Energies

Analyses for FMO

Periodic Boundary Conditons (PBC)

Geometry Optmizatons

Molecular Dynamics (MD)

Hessians, IR and Raman Spectra

Chemical Reactons

• Building up complexity:

Parametrized Methods

Unrestricted (UHF) and Open-Shell (ROHF) Methods

Electron Correlaton

Multconfguratonal Self-Consistent Field (MCSCF)

Electronic Excited States

Multple Layers

Frozen Domain (FD)

Molecular Orbitals and Their Energies (LCMO)

Propertes on a Grid

Struggling with Convergence

Fragmentaton

• Advanced Techniques:

How to compute polarizaton energies

Embedding types

Difuse basis sets

Dual basis sets (AP)

Restartng jobs

Using FMO for non-FMO tasks

Temperature, entropy, and free energy

Acceleraton tricks

How to calculate millions of atoms

Improving GDDI performance

• Reference Materials:

Conclusions and utlook roubleshootng

Collecton o Sample nput and utput iles

Processing esults

G Elish ictonar

Suggestons or urther eading