Using xtb

Getting Help

To get help and an overview of the different flags available in xtb, you can refer to the documentation or use the following command:

xtb --help

Input File

xtb supports various molecular structure file formats:

For periodic calculations, only the Turbomole, VASP POSCAR/CONTCAR, and genFormat files are supported. More details on file formats can be found in the documentation.

Calling xtb

The simplest way to start an xtb calculation requires only a structure file in one of the supported formats, e.g.,

xtb struc.xyz

To perform specific calculations or access different functionalities, you can use various command-line flags when running xtb. These flags will be introduced in the following exercises. Many of them can also be combined, allowing you to, for example, perform a geometry optimization with an implicit solvent model.

Charges and Unpaired Electrons

xtb supports charged molecules as well as molecules with unpaired electrons. You can define charges and the number of unpaired electrons either via command-line flags (--chrg <INT> and --uhf <INT>) or by placing a .CHRG or .UHF file in the working directory, each containing only the respective value.

Available Methods

xtb supports the GFN2-xTB, GFN1-xTB, and GFN-FF methods. By default, GFN2-xTB is used. Other methods can be employed by providing the corresponding flag:

xtb struc.xyz --gfn2
xtb struc.xyz --gfn1
xtb struc.xyz --gfnff

Additional Input File

While xtb has robust default settings, you may need to adjust parameters for certain calculations. This can be done by providing an additional input file:

xtb struc.xyz --input <xtb.inp>

These input files can contain multiple blocks, each beginning with a keyword (e.g., $md), followed by various settings, and ending with $end. For instance, to set the time and temperature for a molecular dynamics (MD) simulation, you can use the following input file:

$md
   time=10 #ps
   temp=200 #K
$end

More detailed settings will be explained in the respective exercises.

Constraining and Fixing Structures

The additional input file also allows you to constrain specific bonds and angles This is very important when you want to maintain certain bonding motifs during optimization or MD simulations. A constraint block might look like this:

$constrain
   distance: 1, 2, 1.4
   angle: 5, 7, 8, auto
   dihedral: 3, 4, 1, 7, 180
$end

Here:

• The distance of atoms 1 and 2 in the input file is constrained to 1.4 Angsröm.
• The angle between atom 5,7, and 8 is constrained to the current angle (due to the auto keyword).
• The dihedral angle between the atoms 1, 3, 4, and 7 is constrained to 180°.

You can also constrain atoms relative to each other using the atoms: keyword (for specific atom indices) or the elements: keyword (for all atoms of a given element). For example:

$constrain
   atoms: 11,12,1-3
   elements: C,N
$end

This constrains atoms 1, 2, 3, 11, and 12 relative to each other, as well as all carbon and nitrogen atoms. If constraints are not sufficient, you can use the $fix block with the atoms: or elements: keywords to completely fix atomic positions in Cartesian space. However, this only applies to geometry optimizations and does not work for MD simulations. More details can be found in the documentation.

Restarting a xtb calculation

For every calculation, a xtbrestart file is written. When this file is in the directory when starting a new xtb calculation, it will automatically be read and xtb tries to use the information to restart a calculation, e.g., a converged Wavefunction.