Published August 18, 2020 | Version v1
Dataset Open

3x 5 µs all-atom MD trajectories; AMBER ff99SB*-ILDN & TIP4P/2005; T4 Lysozyme; 'Fitting side-chain NMR relaxation data using molecular simulations'

Creators

  • 1. University of Copenhagen
  • 2. Ruhr University Bochum

Description

Simulation data for "Fitting side-chain NMR relaxation data using molecular simulations" (https://doi.org/10.1101/2020.08.18.256024).

  • 3 x 5 µs all-atom MD simulations of T4 Lysozyme
  • Force field: AMBER ff99SB*-ILDN with modified methyl rotation barriers1
  • Water model: TIP4P/2005
  • Compressed protein coordinates saved every 1 ps to enable calculation of side-chain NMR relaxation parameters

Contains:

  • 3 x GROMACS .xtc trajectory files for 3 independent simulations
  • 3 x corresponding GROMACS .tpr topology files

1 Hoffmann, F., Mulder, F. A. A., & Schäfer, L. V. (2018). Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. The Journal of Physical Chemistry B, 122(19), 5038–5048. https://doi.org/10.1021/acs.jpcb.8b02769

Files

Files (153.5 GB)

Name Size Download all
md5:dd51d8afdc51b3fa0fad97e30d068a1d
2.3 MB Download
md5:e6ff69a2f28d70a8d908d3263d9a5af0
51.3 GB Download
md5:15c58cff51eb3b4b57f58b4a605937bf
2.3 MB Download
md5:e436f20be0b9276cb0fdd7640c8ef717
51.3 GB Download
md5:322d96a7bf5ebc42f4aa4cf140cdecda
2.3 MB Download
md5:a683da009b75b68ea356916030d67058
51.0 GB Download

Additional details

Related works

Is supplement to
Preprint: 10.1101/2020.08.18.256024 (DOI)