Due to the nature of MD simulations, the computational requirements of the workflow are dependent on the overall size of the protein structure and can grow to become quite significant, even on high performance infrastructures. varMDsim With the minimal input of a PDB formatted protein structure file and simulation time in nanoseconds, the varMDsim module will generate a solvated, ionized water box around a mutated protein structure, create the configuration files for the all-atom, explicit solvent simulation with periodic boundary conditions, and compile the results for downstream analysis.
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SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants.
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