Create D-NEMD_spike.yml

data/simulations/D-NEMD_spike.yml

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+type: md
+title: Nonequilibrium simulations of the glycosylated SARS-Cov-2 ancestral spike
+description: Dynamical nonequilibrium MD (D-NEMD) simulations of the glycosylated and cleaved at the furin site ectodomain of the SARS-CoV-2 ancestral spike
+creator: A.S.F. Oliveira
+organization: University of Bristol
+lab: Oliveira and Mulholland Labs
+models:
+    - 7JJI
+proteins:
+    - spike
+structures:
+    - https://www.rcsb.org/structure/7JJI
+files:
+    - https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/D-NEMD_glycosylated_spike/D-NEMD_simuls.tar.gz
+trajectory: https://molssi-bioexcel-covid-19-structure-therapeutics-hub.s3.amazonaws.com/MulhollandGroup/D-NEMD_glycosylated_spike/D-NEMD_simuls.tar.gz
+size: 8.4 GB
+length: 210 D-NEMD replicates, 10 ns each
+ensemble: NPT
+temperature: 310
+pressure: 1
+solvent: water
+forcefields:
+    - CHARMM36m
+references:
+    - Oliveira, ASF et al. Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike, 2024, eLife
+publication: https://doi.org/10.7554/eLife.97313.1