The PLUMED Consortium
Published June 14, 2022 | Version v1
Dataset Open

Exploration, representation and rationalization of the conformational phase-space of N-glycans

Authors/Creators

  • 1. Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes,University of Bremen, 28359 Bremen, Germany
  • 2. Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy

Contributors

  • 1. Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes,University of Bremen, 28359 Bremen, Germany

Description

Collection of structure and trajectory files of free N-glycans simulated in solution using either the CHARMM36m or GLYCAM06j force field. Simulations are either plain MD or enhanced sampled via the combination of replica exchange methods REST-RECT.

Files

Files (1.4 GB)

Name Size
md5:799627fef9506e104a27d54a17bfa006
108.2 MB Download
md5:64333448a9700990c95aab269190f320
108.6 MB Download
md5:19a38770cc63bad7ccdb2b41d69b6035
214.1 MB Download
md5:6c0acd2ffcc850efb566bc822a6d6ad4
215.2 MB Download
md5:cf083df93430ec66421bd11dfc53c48f
137.8 MB Download
md5:0fddf707188c114a74945e72745636f2
123.3 MB Download
md5:14cf2ffd5d7005f6b7da87e1ceb5ba8e
123.9 MB Download
md5:0861bc4485f0c2569b7f2a1eef1c22ac
183.8 MB Download
md5:9514be70640e01b71cfe8fe95cfbef28
185.1 MB Download

Additional details

Related works

Cites
Journal article: 10.1021/ct5009087 (DOI)
Journal article: 10.1021/jp204407d (DOI)

Funding

European Commission
HPC-EUROPA3 - Transnational Access Programme for a Pan-European Network of HPC Research Infrastructures and Laboratories for scientific computing 730897

References

  • Gil-Ley, A. & Bussi, G. Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering. J Chem Theory Comput 11, 1077–1085 (2015).
  • Wang, L., Friesner, R. A. & Berne, B. J. Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B 115, 9431–8 (2011).