All tutorials have been updated for GROMACS version ! Lysozyme in Water: The intent of this tutorial is to give new users a basic introduction into the. Molecular Simulation. Methods with Gromacs. Hands-on tutorial. Introduction to Molecular Dynamics: Simulation of Lysozyme in Water. Another lysozyme tutorial – focused on details of the topology and Building biphasic systems – a cyclohexane/water layer system, with tips for.
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This is because pdb files often contain ambiguous data, such as two alternative coordinates for the same atom. Also using x-ray crystallography the positions of hydrogens cannot be observed directly. The positions of the hydrogens have either been modelled or are simply not included in the structures.
In the Gromos96 force field, that we will use, polar and aromatic hydrogens are treated explicitly and must be generated if necessary. In contrast, non-polar hydrogens bound to carbon are treated implicitly and must be removed if present in the pdb file.
The conversion program pdb2gmx checks each residue in the structure file against a database and adds hydrogens as appropriate. The program pdb2gmx also creates a topology file for the molecules which contains a description of the connectivity interactions between the atoms. This shows a description of the program and the options available. For example, it is possible to change the hydrogens to deuterium by changing the mass. Most of these options are not important in the current context.
For the conversion of the structure file 1AKI. This will first show the description of the program and generate a warning. The program will ask to select a force field:.
The program generates a string of output to the screen. Look at this output. First you will see that that the program has taken a series of default options. What does the program assume in regard to the pH of the system?
A major limitation of classical simulations is that the protonation states of particular residues must be predefined.
Step 1: Conversion of the PDB File
What would need to be changed to simulate this system at pH 2. When the program has finished, list the files in your directory ‘ ls ‘. You should see four files, the original pdb file, and 3 files generate by pdb2gmx. These are the lysizyme. This file is created automatically together with the topology and contains information that can be used to restrain the positions of the atoms in the structure if needed.
For a more detailed description of these files follow this link. You will see that the. In particular it contains the same information regarding the positions of the atoms, but the layout is different, hydrogens have been added and units have been converted to nm.
Now examine the topology file ‘ more aki. This file contains information describing the molecule and its interactions including the names, types, masses and charges of each atom, as well as information on the bonds, angles, dihedrals, etc between atoms. We now have converted the structure into an appropriate form, hydrogens have been added and generated a topology file that describes the interactions between the atoms. The next step is to minimize the energy of the system.
Normally, the system needs to be energy minimised before it is possible to perform a molecular dynamics simulation in order to remove any local strain. Localized strain can be present due to small errors in the original structure such as bad Van der Waals contacts atomic overlap. Even small differences between the force field used to refine pdb structure and Gromos force field can give rise to unrealistically high forces between atoms. Such strain can be removed by energy minimization of the structure.
The system can be energy minimized using the program ‘ mdrun ‘. This is the same program that will be used to perform molecular dynamics simulations. Mdrun uses a single file called a. This must be copied into your personal subdirectory. The file can also be found here for people who do not have access to the network. You will need to edit the contents of this file use either nedit minim. Modify the title to include you name and the date.
As you can see the file contains a range of parameters.
A full list of all the parameters and the options that can be used in an. Grompp also tutoriap a number of hidden files containing critical information not in the other files.
What information is missing? The program mdrun must get all information regarding nature of the molecule from the.
Look again at the.
This is a so called binary file and is not in a human readable form. To view the contents of this file you can use the command ‘ gmxdump -s eminput. Looking at lysozyyme file will help you answer question 2.
The basic options for the mdrun program can be viewed using:. The -s option is obligatory and followed by the name of the run input file.
Output is generated by specifying the -o, -c and -e options. This will create wate trajectory file, a structure file of the minimized structure and an energy file, with all the energies for every step.
Perform the run using the following command the -v option is used to output all messages to the screen and the option -nice sets the priority level:. The energy minimization may take some time, depending on the CPU in grokacs the load of the computer. The trajectory file is not very important in energy minimizations, but the generated structure file lysozhme.
During the minimization the potential energy decreases. This program also has several options:. Note, in the latest version of the program the numbers are not shown and you must copy and past the key words. Select 9 potentialwhich codes for the total potential energy and then type either a 0 or enter to finish the wafer, thus:. It is also possible to select more than one option, e.
Help on this program can be found at http: The current graph has an error in it, the label for the horizontal axis should be ‘step’ instead of ‘time ps ‘.
Correct this by going to ‘plot’, select ‘axis properties’ and in ‘label string’ delete Time ps and write Step. Then click Accept and Close. To exit xmgrace go to File and select Exit. How long did the system take to converge has it converged? It this structure likely to be the global energy minima?
If not why not? The system you have just minimized contains the protein plus a small number of water molecules. Effectively you have removed one molecule from tutodial crystal latice and performed the minimization in vacuum. In order to be able to simulate the protein in a more realistic environment i. Use a standard cubic box and be sure that the protein does not see its images.
For this the minimum distance between the wall of the box and any atom of the protein must be greater than half of the cut-off 1. Then the program removes any solvent molecules which lie within a certain cutoff distance the sum of the van der Waals radii of any atom of the protein.
We will use water as the solvent. There are, however, many different models to describe water. The topology file aki.
Look breifly at the new version of aki. We now need to mimimize the system again. Follow the same steps as above. You will need to use grompp to generate the mdrun input file. The file can also be found here for people who don’t have access to the network. Tutkrial should note that the option for periodic boundary conditions pbc has now been activated. You will will need to add in appropriate values for the the number of steps of energy minimization to be performed nsteps and the frequency with which the energies and coordinates are written nstenergy and nstxtcout.
Tuotrial should also change the title. As noted above a full list of lyaozyme the parameters and the options that can be used in an. The files needed to performing an MD simulation are very similar to those used to perform the energy minimization although in this case we will use the structure file generated after minimization minimized.
The topology file is the same aki. We run a short initial simulation of 50 ps. This file has information on settings to use for the simulations: You will notice there are a number of additional parameters.
The integrator has been changed to md.
Tutorials – Gromacs
The time step is set to 0. The temperature is set to K. The pressure is set to 1 atmosphere. We also need to generate velocities. This is done using a random number gnerator for which you will need to give a new initial seed a 5 figure number.