分子模拟一般性步骤.docVIP

Below is presented a generalised procedure for performing a simulation. The exact steps and processes involved will vary depending on exactly what is being attempted. Use as a general guide only! 1 Clearly identify the property / phenomena of interest to be studied by performing the simulation.2Select the appropriate tools to be able to perform the simulation and observe the property / phenomena of interest. It is important to read and familiariseyourself with publications by other researchers on similar systems. Tools include: - software to perform the simulation with, consideration of force field may influence this decision.- force field which describes how the atoms / particles within the system interact with each other. Select one that is appropriate for the system being studied and the property / phenomena of interest. Very important and non-trivial step!3Obtain / generate the initial coordinate file for each molecule to be placed within the system. 4Generate the raw starting structure for the system by placing the molecules within the coordinate file as appropriate. Molecules may be specifically placed or arranged randomly. 5Obtain / generate the topology file for the system, using (for example) pdb2gmx, PRODRG or your favourite text editor in concert with chapter 5 of the GROMACS Manual. 6Describe a simulation box (e.g. using editconf) whose size is appropriate for the eventual density you would like, fill it with solvent (e.g. using genbox), and add any counter-ions needed to neutralize the system (e.g. using grompp and genion). In these steps you may need to edit your topology file to stay current with your coordinate file.7Run an energy minimisation simulation on the system (using grompp and mdrun). This is required to sort out any bad starting structures caused during generation of the system, which may cause the production simulation to crash. 8Select the appropriate simulation parameters for the equilibration simulation (