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xTB#

xTB short introduction#

  1. Make xtb.slurm batch script for parallel calculations:

    Bash
    #!/bin/bash
#SBATCH --job-name=xTB-test
#SBATCH --mem=2GB
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=24
#SBATCH -t 1-00:00:00
#SBATCH --partition=common

module load rocky8/all
module load xtb-crest/6.7.0-crest3.0

#Run calculations 
xtb struc.xyz --opt tight --cycles 50 --charge -0 --alpb toluene --gfn 2 -P 4 > final.out

  2. Copy job-input file struc.xyz

  3. Submit the job on base:

    Bash
    sbatch xtb.slurm

xTB long version#

Extended tight binding - xTB program developed by Grimme's group for solutions of common chemical problems. The workhorses of xTB are the GFN methods, both semi-empirical and force-field. The program contains several implicit solvent models: GBSA, ALPB. xTB functionality covers single-point energy calculations, geometry optimization, frequency calculations, reaction path methods. Also allows to perform molecular dynamics, meta-dynamics, and ONIOM calculations. More about xTB on HPC can be found here.

Environment#

Environment is set up by the commands:

Bash
module load rocky8/all
module load xtb-crest/6.7.0-crest3.0

Running xTB jobs#

Input file should be in .xyz format and is executed by the command xtb. This command is usually placed in slurm script.

Bash
xtb struc.xyz --opt tight --cycles 50 --charge -0 --alpb toluene --gfn 2 -P 4 > final.out

In xTB calculation options are specified as command line arguments. -P is number of processors used, --gfn 2 -- calculation method (here GFN2-xTB), --alpb toluene -- ALPB implicit solvation model for toluene. More about command line arguments.

Time & Memory#

Calculation time depends on size of molecule and methods used, and can only be determined empirically.

1 GB per 2 or even more cores should be sufficient. For more detailed information look slurm-XXX-.stat file after a test run. The lines "CPU Efficiency:" and "Memory Efficiency:" will give an idea of ​​how efficiently the resources were used.

How to cite#

The main publication for the xTb program - DOI: 10.1002/wcms.1493.