Introduction to Molecular Dynamics with GROMACS

3. Install Gromacs from a package, or compileit the same way as FFTW.4 . I n s t a l l P y M o l f r o m t h e w e b s i t ehttp://www.pymol.org, or alternatively VMD.Initial input data:Interaction function V(r) - "force field"coordinates r, velocities v5. Install the 2D plotting program Grace/xmgrace. Depending on your platform youmight have to install the Lesstif (clone of Motif)libraries first (www.lesstif.org), and then getthe Grace program source code from the sitehttp://plasma-gate.weizmann.ac.il/Grace/.6. To create beautiful secondary structureanalysis plots, you can use the program “DSSP”from http://swift.cmbi.ru.nl/gv/dssp/. This isfreely available for academic use but requires alicense, so we will use the Gromacs built-in alternative“my_dssp” for this tutorial.If you are following this exercise as part of a labcourse, the installation might already have beendone for you.Compute potential V(r) andforces F i=iV(r) on atomsUpdate coordinates &velocities according toequations of motionCollect statistics and writeenergy/coordinates totrajectory filesMore steps?YesRepeat for millions of stepsThe PDB Structure - thinkbefore you simulate!The first thing you will need is a structure ofthe protein you want to simulate. Go to theProtein Data Bank at http://www.pdb.org, andDone!search for “Lysozyme”. You should get lots of hits, many of which were determined with bound ligands,mutations, etc. One possible alternative is the PDB entry 1LYD, but feel free to test some other alternativetoo.It is a VERY good idea to look carefully at the structure before you start any simulations. Is the resolutionhigh enough? Are there any missing residues? Are there any strange ligands? Check both the PDBweb page and the header in the actual file. Finally, try to open it in a viewer like PyMOL, VMD, orRasMol and see what it looks like. In PyMOL you have some menus on the right where you can show(“S”) e.g. cartoon representations of the backbone!Creating a Gromacs topology from the PDB fileWhen you believe you have a good starting structure the next step is to prepare it for simulation.What do we need to prepare? Well, for instance the choice of force fields, water model, charge states oftitratable residues, termini, add in the missing hydrogens, etc. You will fairly quickly realize that most ofthis stuff is static and independent of the protein coordinates, so it makes sense to put it in a separatefile called a “topology” for the system. The good news is that Gromacs can create topologies automaticallyfor you with the tool pdb2gmx.There are several places where you can find documentation for the Gromacs commands. You shouldalways get some help with “pdb2gmx -h”, which first includes a brief description of what the programNoFig. 3: Simplified flowchart of a standard moleculardynamics simulation, e.g. as implemented in Gromacs.