Molecular Simulation Methods with Gromacs

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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
emtol = 10 ; stop if forces reach this valueemstep = 0.01 ; minimization step sizenstxout = 1 ; compressed traj. output every stepnstenergy = 1 ; energy output every steprlist = 1.0 ; calculate interactions up to 1nmcoulombtype = pme ; use PME for electrostaticsvdw-type = cut-off ; simply cut off the LJ interactionsrvdw = 1.0 ; cut-off range for LJ interactionsconstraints = none ; we use flexible bondsdefine= -DFLEXIBLEThese settings are for a steepest-descent minimization for 500 steps, or until forces of10 kJ mol -1 nm -1 (the standard Gromacs force units). The configuration and systemenergies will be output every step, and the cut-offs will be at 1nm. PME will be used forelectrostatics. The flexible bonds are turned on by disabling constraints, and defining anpreprocessor directive ‘-DFLEXIBLE’ to ensure that the force field included in thetopology gives flexible bonds.Run the equilibration by preprocessing the input files into a run file withgrompp -f em_flexible.mdp -c solvated.gro -o em_flexible.tprwhich generates the run file em_flexible.tpr. Run this file withmdrun -v -deffnm em_flexibleand do the next step, minimization with constrained (held at fixed distance) bonds. Forthis we use em.mdp:integrator = steepnsteps = 500emtol = 10emstep = 0.01nstxout = 1nstenergy = 1rlist = 1.0coulombtype = pmevdw-type = cut-offrvdw = 1.0constraints = all-bonds ; all chem. bonds are constrainedwhich differs only from em_flexible.mdp in the last two lines. We run in a similarway:grompp -f em.mdp -c em_flexible.gro -o em.tpr
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Molecular Simulation Methods with Gromacs

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