Molecular Muscles

Molecular muscles belong to the class of molecular machines which won the Nobel Prize in 2014. Computational approaches to molecular machines are challenging due to the vast conformational flexibility and limited experimental structure determination common to most supramolecular assemblies. As part of workflows you may need to scan coordinates at a time, e.g., angles, distances, or relative orientations. Here, we will perform a constrained distance scan to disentangle a molecular muscle.

Constrained Scan

Apart from the molecularmuscle.xyz structure file you need two additional input files: xcontrol instruction set and .CHRG file to define total charge:

xtb molecularmuscle.xyz -I xcontrol --gfnff --opt --alpb dmso > scan.out &

Watch the scan (with e.g. molden) in the xtbscan.log file and determine the two native resting positions of the molecular muscle and when it starts to break apart artificially.

Optional

Try the scan with maxcycle=5 and see what happens. This reduces the number of optimization steps for each point in the PES scan to speed up the scan.