Molecular Simulation Methods with Gromacs

Preparing the systemWe will start with a topology that can be downloaded from http://www.gromacs.org/Documentation/Tutorials/Free_energy_of_solvation_tutorial: getthe archive file fe-tutorial-4.6.tar.gz from the bottom of the page, or dowget http://www.gromacs.org/@api/deki/files/194/=fe-tutorial-4.6.tar.gzThen extract the archive withtar xzvf fe-tutorial-4.6.tar.gzand look for a file named topol.top, and a very basic coordinate file namedethanol.gro. This topology uses the OPLS force field and defines a methanemolecule, and includes the definitions for SPC/E water.Question: Take a look at the topology file topol.top. For the ethanol moleculedefinition, can you find which atoms are there, and how they are connected?We will first prepare the simulation box: the original configuration file has a dummysimulation box associated with it (you can see that by looking at the file ethanol.gro).We do this with:editconf -f ethanol.gro -o box.gro -bt dodecahedron -d 1which sets up the simulation box. In this case, it will make the simulation box a rhombicdodecahedron with a minimum distance between the solute (the ethanol molecule) andthe box edge of 1nm. The box is a rhombic dodecahedron because it provides a moreeffective packing of periodic images than rectangular boxes: we can use fewer watersfor the same distance between periodic images of the ethanol molecule. See theGromacs manual for illustrations of this box shape and how its periodic images arearranged.Next, we solvate the system in watergenbox -cp box.gro -cs -o solvated.gro -p topol.topThis should generate a system with 310 water molecules taken from the default filename of the -cs option: a box of equilibrated water molecules.To make the configuration suitable for simulation, we will first minimize its energy,twice: once with flexible bonds, and once with constrained bonds. For the flexible-bondminimization we will use the following settings (see the included fileem_flexible.mdp)integrator = steep ; steepest-descent minimizationnsteps = 500 ; max. number of steps