The CHARMM Water-Box Tutorial

The CHARMM Water-Box TutorialContents1 Aim of the Tutorial 12 Getting Started 12.1 Interactive Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12.2 Batch Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22.3 CHARMM Style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Building a Water Molecule 33.1 Residue Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33.2 Parameter Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53.3 Generating Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63.4 Write the Output Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 Molecular Dynamics Simulations 94.1 Building a Cube of Water Molecules. . . . . . . . . . . . . . . . . . . . . . . . . 94.2 Adding Periodic Boundary Conditions . . . . . . . . . . . . . . . . . . . . . . . 124.3 Analysing the Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 Web Links 15Computational Chemistry Module1 Aim of the TutorialInthistutorialyouwillfirstbuildasimplemolecularsystemandthencombineseveralmoleculestogether which will be used to run a molecular dynamics simulation.To successfully complete the tutorial, the following steps should be carried out in order:1. Generate a water molecule2. Build a system of 32 water molecules3. Run a molecular dynamics simulation2 ...