Molecular Dynamics files for "Mechanistic snapshots of lipid-linked sugar transfer" by Morgan et al.

LEGEND: MODEL_01 :: substrate-bound MODEL_03 :: pre-catalysis MODEL_04 :: product-bound #---------------------# Unbiased MD Simulations MODEL_0*/PROD/step*mdp :: Gromacs MDP files for the equilibration and production by CHARMM-GUI MODEL_0*/PROD/index.ndx :: Gromacs index files with the groups definition MODEL_0*/PROD/topol.top :: Overall topology files of the MD system MODEL_0*/PROD/toppar :: folders containing the .itp files of the topology and parameters for the single molecules MODEL_0*/PROD/step5_input.gro :: initial all-atoms MD boxes MODEL_0*/PROD/step6.6_equilibration.gro :: equilibrated systems MODEL_01/PROD/reduced.stride.xtc :: extracted trajectories of the protein, substrates, and products MODEL_01/PROD/reduced.gro :: reduced GRO files to open the reduced.stride.xtc #---------------------# Steered MD MODEL_0*/SMD_*/model_0*.equilibrated.gro :: initial MD box for the Steered MD MODEL_0*/SMD_*/plumed.dat :: PLUMED files with the setting and selections for the SMD MODEL_04/SMD_*/smd.mdp :: Gromacs MDP file for the production MODEL_04/SMD_*/index.ndx :: Gromacs index file with the groups definition MODEL_0*/SMD_*/topol.top :: Overall topology file of the MD system MODEL_01/SMD_*/toppar :: folders containing the .itp files of the topology and parameters for the single molecules MODEL_04/SMD_*/REP_*/reduced.* :: extracted trajectories of the protein, substrates, and products (3 Replicas per system)