Input Generator

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• Quick MD Simulator
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Quick MD Simulator

The Quick MD Simulator helps you to generate a series of CHARMM inputs for molecular dynamics simulations of your molecule in aqueous solvent environments. The following is a brief description for each step:

• STEP1: Read biomolecular coordinate
  You can download a coordinate from RCSB (PDB website) or upload a PDB file (RCSB or CHARMM formats) from your local machine.
  
  
• STEP2: Solvate the biomolecule
  The biomolecule will be solvated with water molecules in this step. You can choose a shape (Rectangular or Truncated Octahedral [Octagonal]) of the system. You can specify the system dimension or let CHARMM to determine the system size based on the biomolecular extent. It is this step to add ions to neutralize the system.
  
  
• STEP3: Setting periodic boundary conditions
  The periodic boundary conditions are applied based on the system shape and size. And, FFT grid information of the Particle-mesh Ewald (PME) method is determined. Short steps of minimization are performed to remove bad contacts. You can increase the step later to minimize the system longer.
  
  
• STEP4 and 5: Equilibration and Production
  While NVT (constant volume and temperature) is used for equilibration (step4), you can specify either NVT or NPT (constant pressure and temperature) dynamics for production runs (step5). Because of excessive computing powers required for long simulations, you need to download the equilibration and production input files and run them on your local machines. You may want to change number of MD steps (nstep), print-out frequency (nprint), and the trajectory saving frequency (nsavc) for postprocessing of simulation runs.