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Description / Information

Structures.

If used for publication, please cite the following reference:

F. H. Bangerter, M. Glasbrenner, C. Ochsenfeld,
"Low-scaling Tensor Hypercontraction in the Cholesky Molecular Orbital Basis Applied to Second-Order Møller-Plesset Perturbation Theory",
J. Chem. Theory Comput., 17, 211-221 (2021).

Download vitk2_tar.gz (36 kB)

Description / Information

Structures, initial conditions, and movies.

If used for publication, please cite the following reference:

L. D. M. Peters, J. Kussmann, C. Ochsenfeld,
"Combining Graphics Processing Units, Simplified Time-Dependent Density Functional Theory, and Finite-Difference Couplings to Accelerate Nonadiabatic Molecular Dynamics",
J. Phys. Chem. Lett., 11, 3955-3961 (2020).

Download namd2_tar.gz (7 MB)

Description / Information

PDB file of Sirtuin 5.

If used for publication, please cite the following reference:

B. von der Esch, J. C. B. Dietschreit, L. D. M. Peters, C. Ochsenfeld, J. Chem. Theory Comput., 15, 6660-6667 (2019).

Download sirt5.pdb (5 MB)

Description / Information

Movies, initial conditions, and energy plots of the NAMD simulations. Molecular structures used for the timings.

If used for publication, please cite the following reference:

L. D. M. Peters, J. Kussmann, C. Ochsenfeld, J. Chem. Theory Comput., 15, 6647-6659 (2019).

Download namd_tar.gz (134 MB)

Description / Information

An hands-on tutorial for identifying free energy hot-spots in molecular transformations, including scripts and an example.

If used for publication, please cite the following reference:

J. C. B. Dietschreit, L. D. M. Peters, J. Kussmann, C. Ochsenfeld, J. Phys. Chem. A , 123, 2163 (2019).

Download hot-spots_tar.gz (271 kB)

Description / Information

Molecular structures that were used to benchmark the influence of the gauge origin on the electronic g-tensor.

If used for publication, please cite the following reference:

M. Glasbrenner, S. Vogler, C. Ochsenfeld, J. Chem. Phys. 150, 024101 (2018).

Download g-tensor.tar.gz (48 kB)

Description / Information

Molecular structures that were used to analyze the impact of preselective screening in O(N) exact exchange gradient calculations.

If used for publication, please cite the following reference:

J. Kussmann and C. Ochsenfeld, J. Chem. Theory Comput. 11, 918-922 (2015).

Download prelink_grad_structures.tgz (39 kB)

Description / Information

Molecular test sets for ¹⁹F-, ¹⁷O-, ³¹P- and ¹⁵N-NMR shifts.

The structures were optimized at the CCSD(T)/cc-pVTZ level (see publication for further details).

If used for publication, please cite the following reference:

M. Maurer and C. Ochsenfeld, J. Chem. Theory Comput. 11, 37 (2015)

Download nmr-benchmark-set-f-n-o-p.tgz (4 kB)

Molecular structures for benchmarking NMR shifts

Description / Information

A molecular test set covering a broad range of the NMR scale for hydrogen and carbon shifts with high relevance to organic chemistry.

The global minimum structures were obtained at the CCSD(T)/cc-pVTZ level (see publication for further details).

If used for publication, please cite the following reference:

D. Flaig, M. Maurer, M. Hanni, K. Braunger, L. Kick, M. Thubauville, and C. Ochsenfeld, J. Chem. Theory Comput. 10, 572 (2014)

Download nmr-benchmark-set.tgz (3 kB)

Description / Information

A set of structures for benchmark/testing of integral screening methods and other approximations for large systems. The set contains insulating, delocalized, radical, and ionic systems with medium to very large systems up to 1707 atoms.

If used for publication, please cite the following reference:
S. A. Maurer, D. S. Lambrecht, D. Flaig, and C. Ochsenfeld, J. Chem. Phys. , 136, 144107 (2012).

Reference data is presented in the corresponding supplementary material.

Download benchmark_set.tgz (339 kB)

Description / Information

HF/6-31G** optimized capped oligoprolines AcN−[Pro]₁₅−CONH₂ and AcN−[Pro]₁₅−CO₂CH₃ for PP1 and PP2 helical arrangement of the backbone. The initial structures were generated using the program package Maestro assuming idealized dihedral angles for the respective helix backbone
(for PPI: φ = -75°, ψ = 160°, ω = 0° and
for PPII: φ = -75°, ψ = 145°, ω = 180° ).

If used for publication, please cite the following reference:
M. Kuemin, S. Schweizer, C. Ochsenfeld, and H. Wennemers, J. Am. Chem. Soc. , 131, 15474 (2009).

Download pp_structures.tgz (112 kB)

Description / Information

Structures of amylose chains containing n=1,2,4,8,16,32,48,64 -D-glucose units. The original structures have been obtained by the SWEET tool [A. Bohne, E. Lang, and. C. W. von der Lieth, J. Mol. Model. 4, 33 (1998); A. Bohne, E. Lang, and. C. W. von der Lieth, Bioinformatics 15, 767 (1999)].
The sequence has been reordered by applying the reverse Cuthill-McKee algorithm onto the connectivity matrix.

If used for publication, please cite the following reference:
J. Kussmann and C. Ochsenfeld, J. Chem. Phys. 127, 054103 (2007).

• readme.txt (828 B) (right-click, "save as")
• -D-glucose (1 kB)
• 2 (1-4)-connected -D-glucose units (2 kB)
• 4 (1-4)-connected -D-glucose units (4 kB)
• 8 (1-4)-connected -D-glucose units (7 kB)
• 16 (1-4)-connected -D-glucose units (13 kB)
• 32 (1-4)-connected -D-glucose units (28 kB)
• 48 (1-4)-connected -D-glucose units (48 kB)
• 64 (1-4)-connected -D-glucose units (57 kB)

• Complete directory as tar-ball (57 kB)

Structures of linear n-alkanes C_nH_2n+2 with n=10,20,40,80,160. (9 kB)

Structures of linear n-alkanes C_nH_2n+2 with n=1,2,3,4,5,6,7,8,9,10,13,15,20,30,40,50,60,80,100,160,300,320. (23 kB)

Structures of glycine chains Gly_n with n=1,2,3,4,5,6,7,8,9,10,20,30,40,50,60,70,80,90. (35 kB)

• SparseCholesky.tgz (7 kB)

• dna_fragments.tgz (34 kB)
• atom-reordered fragments (n=4,8,16) (28 kB)

• peptides_qmmm.tgz (29 kB)