Training Program to Study the Computation of Molecular Reaction Mechanisms using Gaussian on High Performance Computing (HPC) Systems

Submission Number: 188
Submission ID: 4257
Submission UUID: 2a0a3204-cb4e-4cab-9f14-ec4be4a1ce08
Submission URI: /form/project

Created: Tue, 12/12/2023 - 10:39
Completed: Tue, 12/12/2023 - 10:39
Changed: Wed, 09/04/2024 - 15:31

Remote IP address: 128.6.36.25
Submitted by: Udi Zelzion
Language: English

Is draft: No
Webform: Project
Training Program to Study the Computation of Molecular Reaction Mechanisms using Gaussian on High Performance Computing (HPC) Systems
CAREERS
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Project Leader

Alan Goldman
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Project Personnel

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Millie Trusler
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Project Information

We propose to develop an introductory training program, and supplementary monitoring and reporting tools in the form of an interactive Excel spreadsheet. This program is designed for new graduate and undergraduate students to learn how to use computational chemistry software packages on HPC systems. For this purpose, we will be using the Rutgers HPC cluster Amarel and a general purpose computational chemistry package Gaussian. The program will provide a practical workflow for testing various molecular systems and molecular reactions. It will help students develop their skills in computational chemistry and bolster their confidence in creating computations for their own molecular systems. This program will aid in defining and refining the commands and functions in Gaussian that are most commonly used in the field of computational organometallic and organic chemistry. It will also assist in job management and processing on the Amarel cluster and any other HPC system operating with a SLURM scheduler.

Project Information Subsection

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123 Bevier Road
Piscataway, New Jersey. 08854
CR-Rutgers
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Yes
Already behind3Start date is flexible
6
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12/15/2023
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  • Milestone Title: Launch
    Milestone Description: Give a launch presentation during the CAREERS monthly meeting.


    Completion Date Goal: 2023-12-15
    Actual Completion Date: 2023-12-15
  • Milestone Title: Setting up
    Milestone Description: Review literature on computational chemistry, specifically on Density-Functional Theory (DFT). Set up an account on the Rutgers HPC cluster, Amarel, and become familiar with job submission and the Gaussian electronic structure modelling program.
    Completion Date Goal: 2024-01-15
  • Milestone Title: Using Gaussian
    Milestone Description: • Run examples for water molecule optimization, ranging from 1 molecule to an ensemble of 5 molecules. Identify the key parts in the resulting log files
    • Optimize and find the transition states/energies associated with nucleophilic substitution reactions (SN1 and SN2).
    • Create an example of a 2-step mechanism for ring opening from epoxides to alcohols.
    • Optimize transition states of larger molecules using Wilkinson’s Catalyst.

    Completion Date Goal: 2024-04-15
  • Milestone Title: Documentation
    Milestone Description: 4. Set up an interactive Excel sheet with all the examples, outputs and documentation from previous milestones. The Excel sheet will be made available on GitHub serving as a guide for anyone who would like to learn how to run Gaussian and analyze its results.
    Completion Date Goal: 2024-05-15
  • Milestone Title: Warp-up
    Milestone Description: Give a wrap-up presentation at the CAREERS monthly meeting.
    Exit interview with Udi Zelzion.
    Completion Date Goal: 2024-06-15
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The student will learn how to run Gaussian on a HPC system.
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Access to Amarel ,Rutgers' HPC cluster.
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Final Report

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