Quick MD Simulator

    The Quick MD Simulator (http://www.charmm-gui.org/?doc=input/mdsetup) helps you to generate a series of CHARMM and NAMD inputs for molecular dynamics simulations of your molecule in aqueous solvent environments.

    Please note that

    • If you are not familiar with the first PDB reading step, please first watch these video demos.

    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. 

      NAMD inputs (v2.7b3 or after) are provided for equilibration and production
      • Input files can be found in "namd" directory when you download tar archive ("charmm-gui.tgz") after all the input generation.
      • namd/step4_equilibration.inp: use generated coordinates of a protein/water system to perform equilibration. Equilibration inputs use collective variable restraints to slowly release the system to facilitate stable simulation.
      • namd/step5_production.inp: use the restart file from NAMD and continue production runs.

      GROMACS inputs (v5.0 or after) are provided for minimization, equilibration, and production
      • Input files can be found in "gromacs" directory when you download tar archive ("charmm-gui.tgz") after all the input generation. See gromacs/README.
      • gromacs/step4.0_minimization.mdp: use generated coordinates of a protein/water system to perform minimization.
      • gromacs/step4.1_equilibration.mdp: use the minimized coordinate from step4.0 to perform equilibration.
      • gromacs/step5_production.mdp: use the equilibrated coordinate from step4.1 and continue production runs.

      AMBER inputs (v16 or after) are provided for minimization, equilibration, and production
      • Input files can be found in "amber" directory when you download tar archive ("charmm-gui.tgz") after all the input generation. See amber/README.
      • amber/step4.0_minimization.mdin: use generated coordinates of a protein/water system to perform minimization.
      • amber/step4.1_equilibration.mdin: use the minimized coordinate from step4.0 to perform equilibration.
      • amber/step5_production.mdin: use the equilibrated coordinate from step4.1 and continue production runs.

      GENESIS inputs (v1.1.0 or after) are provided for minimization, equilibration, and production
      • Input files can be found in "genesis" directory when you download tar archive ("charmm-gui.tgz") after all the input generation.
      • genesis/step4.0_minimization.inp: use generated coordinates of a protein/water system to perform minimization.
      • genesis/step4.1_equilibration.inp: use the minimized coordinate from step4.0 to perform equilibration.
      • genesis/step5_production.inp: use the equilibrated coordinate from step4.1 and continue production runs.

      OpenMM inputs (v6.2 or after) and running scripts are provided for equilibration and production
      • Input files can be found in “openmm” directory when you download tar archive ("charmm-gui.tgz") after all the input generation.
      • openmm/openmm_run.py: OpenMM running scripts written in python.
      • openmm/step4_equilibration.inp: use generated coordinates of a protein/water system to perform equilibration.
      • openmm/step5_production.inp: use the restart file from OpenMM and continue production runs.

      CHARMM/OpenMM inputs (c39b1 or after) are provided for equilibration and production
      • Input files can be found in “charmm_openmm” directory when you download tar archive ("charmm-gui.tgz") after all the input generation.
      • charmm_openmm/step4_equilibration.inp: use generated coordinates of a protein/water system to perform equilibration.
      • charmm_openmm/step5_production.inp: use the restart file from CHARMM/OpenMM and continue production runs.

    Reference for Quick MD Simulator:

    S. Jo, T. Kim, V.G. Iyer, and W. Im (2008) 
    CHARMM-GUI: A Web-based Graphical User Interface for CHARMM. J. Comput. Chem. 29:1859-1865 

    J. Lee, X. Cheng, J.M. Swails, M.S. Yeom, P.K. Eastman, J.A. Lemkul, S. Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V.S. Pande, D.A. Case, C.L. Brooks III, A.D. MacKerell Jr, J.B. Klauda, and W. Im (2016)
    CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field. J. Chem. Theory Comput. 12:405-413 


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