This tutorial introduces the student to the practice of Molecular Dynamics (MD) simulations of peptides. The protocol used is a suitable starting point for investigation of peptides, provided that the system does not contain non-standard groups. At the end of the tutorial, the student should know the steps involved in setting up and running a simulation, including some reflection on the choices made at different stages. Besides, the student should know how to perform quality assurance checks on the simulation results and have a feel for methods of analysis to retrieve information.
A report is not required for the Structural Biology course. However, you may find the next set of questions useful in developing an understanding of Molecular Dynamics Simulations and the information you can get out of them. If you do want to write a report, it should start with a short introduction of what was the purpose of the work and contain the following elements:
Information about the content of the various files can be found in the online manual at http://www.gromacs.org/Documentation/File_Formats.
What is the scientific background of the Trp-cage design?
What are the number of atoms before and after the conversion with pdb2gmx? Explain the difference.
List the atoms, atom types and charges from a tyrosine residue as given in the topology file
Which method was used for the energy minimization?
How many steps were specified in the parameter file and how many steps did the energy minimization take?
What could cause the energy minimization to stop before the specified number of steps was reached?
What was the final potential energy of the system?
Compare the structures before and after energy minimization by loading them into PyMol. What are the differences?
What is the volume of the cell generated by editconf?
How many water molecules were added to the system and what volume does that amount of water correspond to?
How many atoms were in the system after adding solvent?
Why is it not a problem to have the peptide sticking out of the water?
How many sodium and chloride ions were added to the system?
How many steps were specified in the parameter file and how many steps did the energy minimization take?
What was the final potential energy of the system after energy minimization?
How many steps were specified in the parameter file and how many steps did the minimization take?
What is the final potential energy of the system?
What was the length of the simulation in picoseconds?
How is the inclusion of the position restraints handled in the topology file?
What happened with the temperature during the simulation?
What happened to the potential/kinetic/total energy and how can this be explained?
There are two groups which were separately coupled to a heat bath. Which groups are that and what do you think is in each of these groups?
What happened to the temperature?
What happened to the potential/kinetic/total energy and how can this be explained?
What happened to the temperature during the simulation?
What happened to the pressure during the simulation?
How does the density behave over time?
Why does the density of the system change if pressure coupling is turned on?
How many steps are needed to get a total simulation time of 10 ns?
How many frames are in the trajectory file and what is the time resolution? ( T )
How long did the simulation run in real time (hours), what was the simulation speed (ns/day) and how many years would the simulation take to reach a second? ( T )
Which contribution to the potential energy accounts for most of the calculations?
What happens if the peptide diffuses over the boundary of the box?
What is the average temperature and what is the heat capacity of the system? ( T )
Estimate the plateau values for the pressure, the volume and the density. ( T )
What was the minimal distance between periodic images and at what time did that occur? ( T )
What happens if a cut-off is used for electrostatic interactions and the minimal distance is shorter than the cut-off distance?
Indicate the start and end residue for the most flexible region (not the termini) and the maximum amplitude. ( T )
At what time and value does the RMSD reach a plateau? ( T )
Briefly discuss two differences between the graphs against the starting structure and against the average structure. Which is a better measure for convergence?
At what time and value does the radius of gyration converge? ( T )
Estimate the number of hydrogen bonds within the protein and between protein and solvent over the last nanosecond. ( T )
Discuss the relation between the number of hydrogen bonds for both cases and the fluctuations in each.
What can you say about the stability of the hydrogen bond from this graph?
What can you say about the interactions? The acidic residue is highly conserved and mutation of that aspartate in humans is known to result in prion disease. What could be the cause of that?
Discuss some of the changes in the secondary structure, if any.
What can you say about the conformation of these residues, based on the ramachandran plots (see the plot given above)?
How many transitions do you see?
What are the smallest 1/r^3 and 1/r^6 averaged distances in the simulation? ( T )
Write a concluding paragraph, comparing the results obtained to experimental results.