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Background Equilibration, relaxation and production runs were performed on GPUs using the CUDA version of PMEMD in AMBER 16 and AMBER ff14SB force field. Minimisation steps were performed on a CPU using PMEMD in AMBER 16 and the AMBER ff14SB force field. All software is available from http://ambermd.org/. Contents There are three tarball (.tar.gz) files containing the core simulation data: one for wild type (WT), the second for the I438V A524T mutant and the third for the S449P mutant. Each contains: 1. a source PDB (.pdb) file 2. Five AMBER trajectory (.nc) files for five independent MD simulations, numbered 1 to 5. Note: each of these files is over 2GB. There is an additional tarball containing the control files and scripts used for running the MD simulations: 1. Multiple control (.ctl) files numbered 1 to 10 that are used to minimize (min prefix), relax (rel prefix) and equilibrate (equ prefix) the model 2. Executable do_md that performed all the minimisation, relaxation and equilibration steps 3. control file prod.ctl used for the production run 4. Executable run_prod that was used to perform the production run 5. Two control files (prod_short.ctl and prod_short_2.ctl) for the short runs used to de-correlate the simulation for the independent runs 6. Executable run_short and run_short_2 used to carry out the de-correlated production runs.
hepatitis C virus, MD simulations, E2 glycoprotein, HCV, molecular dynamics
hepatitis C virus, MD simulations, E2 glycoprotein, HCV, molecular dynamics
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