Simulations of Spontaneous TM Domain Dimer Formation
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2017-10-18, 2017-10-18
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Simulations of spontaneous dimer formation of 5 TM domain dimers in DLPC bilayers. Simulations are performed in the coarse-grained scheme using either standard Martini parametrization or its derivative in which the protein–protein interactions (Lennard-Jones epsilons) are downscaled by 10%.
The tar files are named after the PDB codes of the corresponding dimers. Each tar contains 10 replicas (files numbered 1 to 10) for both scaled (S) and unscaled (U) force fields. The trajectory (.xtc, stored every 10ns, solvent omitted), energy file (.edr), and run input file (.tpr) for GROMACS are provided for each replica. The starting structures (.gro) shared by scaled and unscaled are also given. The index file (.ndx) is common for all simulations of the dimer, and the topology files (.top) are given separately for simulations using the scaled and unscaled force fields. The common simulation parameter file (.mdp) is provided. TOP.tar contains all topologies.
The scaling is achieved by adding 'p' to the bead types in the proteins. The corresponding parameters are given in the "martini_v2.2_scaled.itp" file. Note that for uniform style, the unscaled parameters are given in a similar manner in a file "martini_v2.2_unscaled.itp".
For a more thorough explanation of the purporse of the files and the simulation parameters, see the related publication:
Javanainen M, Martinez-Seara H, Vattulainen I (2017) Excessive aggregation of membrane proteins in the Martini model. PLoS ONE 12(11): e0187936. https://doi.org/10.1371/journal.pone.0187936