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MOLECULAR DYNAMICS (NAMD) WORKFLOW
VMD will be used to visualize your molecule, generate psf file and analyze your resulting output files
Search, identify, and download .pbd file for your molecule. Take note of the PDB ID to add to the file record.
Create a protein structure file for your protein.
This will walk you through the process of adding water molecules that will surround your molecule.
This will walk you through the creation of a water box - adding water molecules that surround your molecule in a specific space (box). It is important to record the size of the box you generate as well as the center for (X,Y,Z). This will be used in to identify the size of your simulation box.
This will walk you through the process of running a simulation using periodic boundary conditions. In order to run this simulation, you must know the size of your water box and your simulation box must be able to accommodate the solvated molecule without the molecule being near any side. (visualize this to confirm in VMD.
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