This file was created by Jian-Hao Li on 19 May 2018.

The folder "di-Thy" contains 7 subfolders (for 7 consecutive steps):

1. LST-CG: Input file for the linear synchronous transit calculation followed by conjugate gradient minimisation (LST-CG) between an ideal-B-DNA extracted di-Thy and a geometrically optimised Th<>Th. The obtained structure is used for subsequent constrained ground state optimisation scans of di-Thy and Th<>Th.

2. Constrained Opt: Input files for the constrained optimisation of (2.6,74)di-Thy and (2.2,74)Th<>Th. Other structures in the optimisation scans can be computed similarly.

3. Singlepoint: Input files for valence calculation of all the optimised structures obtained in the optimisation scans of di-Thy and of Th<>Th. Each di-Thy structure is marked by a number between 01-74 (see Map_cell#.pdf in the di-Thy folder) that is then used as the folder name for the di-Thy structure. For Th<>Th, the name "1866Th=Th" denotes (1.8,66)Th<>Th.

4. Cond: Input file for calculating the conduction orbitals of (2.6,74)di-Thy. Other structures are calculated with the same parameter settings.

5. LR_TDDFT: Input file for calculating the linear response TDDFT/TDA of (2.6,74)di-Thy. Other structures are calculated with the same parameter settings.

6. Sys2Ref Projection: Input file for performing projections of the hole (NTO1-H) and electron (NTO1-E) orbitals of the first 8 excitations of (2.6,50)di-Thy onto the corresponding NTOs (NTO1-H and NTO1-E) of the other structures. The thy_dimer_state_labellings.dat is used (put in the same folder before calculation) to set up the initial label given to each excited state of (2.6,50)di-Thy. (If thy_dimer_state_labellings.dat is absent, no initial labels are assigned.) After calculation, thy_dimer_state_labellings.dat.tmp is produced that records the new label for each excited state (the last line). In the current example, the NTOs of (2.6,50)di-Thy (folder name "24") are compared to those of the following folders: 03-13, 15-28, 30-74, 02, 29, and 01 (by setting up qnto_ref_dir accordingly in the input file). It can be seen that the "Old Sys label" are the same as "Sys label", indicating that a self-consistent labelling has been achieved.

7. Linear Int with 2274Th=Th: Input files for performing singlepoint calculation (same parameters as in 3.) of the interpolated structures between (2.2,74)Th<>Th and all the di-Thy structures. Conduction and LR_TDDFT calculations can be performed with the same parameters used in 4. and 5., followed by excited states labelling calculations as in 6.

The folder "dTpdT" contains the calculation input files for the dTpdT molecules. Some naming examples: 2850TT and 2850TT-c respectively denote (2.8,50)dTpdT without/with a truncated response density kernel being used in the TDDFT calculation. Similarly, 2274T=T-c denotes (2.2,74)T<p>T with a truncated response density kernel being used in TDDFT.

The folder "TTTTAAAA" contains the calculation input files for the TTTT/AAAA molecular segment extracted from B-DNA. All ONETEP calculations were performed using version 4.3.0.7.

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